Having led 3-1 from the first leg, Unai Emery’s side were favourites to advance and got the better of a back-and-forth contest, with Aubameyang hitting three to seal a 4-2 win on the night and a 7-3 aggregate success.
In a week of English comebacks in the Champions League, Aubameyang’s goals made sure Arsenal were not on the receiving end of another.
Despite falling behind to Kevin Gameiro’s 11th-minute effort, the Gunners rallied as Aubameyang equalised and Alexandre Lacazette struck to put them ahead on the night and in control of the tie.
Gameiro, who was part of Emery’s Sevilla side who won three successive Europa League titles, continued his fine scoring run in the competition with another – only for Aubameyang to add the gloss with two more efforts.
A disappointing home draw with Brighton last weekend all but ended any hopes of a top-four finish in the Premier League for Arsenal.
Emery, who has not lost a knockout tie in this competition since he was in charge of Valencia in 2012, knows he needs to win the same title in Baku on May 29 to seal a Champions League return for Arsenal in his first season at the helm.
Valencia created the first chance, Laurent Koscielny doing well to beat Rodrigo to Gameiro’s near-post cross.
Goncalo Guedes fired well wide of Petr Cech’s goal when latching onto Ainsley Maitland-Niles’ clearance, the hosts attempting to start in the same manner which saw them race into a lead at the Emirates Stadium.
That goal would come as Arsenal were caught committing too many men forward and Gameiro slid in to tuck home Rodrigo’s cross from close range.
Gameiro then accidentally blocked a Rodrigo strike as Valencia took the game to their visitors.
But, just as with last week’s first leg, Arsenal hit back seemingly from nowhere as Aubameyang ran on to Lacazette’s header and his cool finish levelled the scores on the night.
The equaliser took some of the wind out of the Valencia sails but skipper Dani Parejo came close with a free-kick 10 minutes before the interval.
Lacazette then spurned a marvellous opportunity to all but put the tie beyond Valencia as he could only turn Aubameyang’s pass onto the outside of the post when Arsenal’s player of the season should have done so much better.
He made amends with a fine finish five minutes after the restart, picking up the ball in the box and wriggling free before arrowing a finish past Neto.
Valencia needed four in the final 40 minutes and pulled one back as Gameiro bundled the ball over the line having again accidentally block a Rodrigo strike.
Ezequiel Garay’s long-range strike flew wide as the La Liga outfit sort to make the closing stages more awkward for Arsenal.
Instead, in committing more men forward, they conceded a third, Aubameyang tucking away Maitland-Niles’ cross to the near-post.
He completed his hat-trick with a drilled finish in the closing stages, grabbing his 29th of the season in the process.
There was a skirmish at full-time, with Maitland-Niles booked for his involvement, but it took little shine off a fine evening for Arsenal, who comfortably advance to the final with Emery again proving he is the go-to man in the Europa League.
Jose Mourinho has accused Ajax of naivety after their Champions League collapse against Tottenham.
Ajax’s ambitions of meeting Liverpool in the June 1 final were destroyed as Spurs staged an extraordinary second-half revival in Amsterdam on Wednesday, overturning a 3-0 aggregate deficit to progress on the away goals rule.
Mourinho, a Champions League-winning manager with Porto and Inter Milan, said Ajax’s philosophy was trumped by Tottenham’s strategy at the Johan Cruyff Arena.
And the Portuguese criticised them for treating the second half as if they were “playing against Vitesse in the Dutch league”.
“Every team grows up, you need that base, you need that philosophy, you need that style of play adapted to the quality of the players,” former Chelsea and Manchester United manager Mourinho said in his role as a pundit with BeIN Sports.
“Ajax deserve all the credit for that and all the admiration of people like us who love football, and we give them the credit they deserve.
“But football is a sporting battle and in battles you need strategy and to win matches, especially special matches, for special matches you need sometimes not to be tied to your philosophy.
“You need sometimes to go against your philosophies to win a football match and I think if Ajax, in the second half, hide their weaknesses better, but everybody knows their weaknesses, they have to cope with that.”
Ajax started their Champions League campaign over nine months ago on July 25, with a 2-0 win over Austrian outfit Sturm Graz in the second round of qualifying.
Erik Ten Hag’s side became the first to reach the semi-final of the competition after playing in three qualifying rounds, and thrillingly humbled holders Real Madrid and Juventus in the knockout stages.
Barcelona-bound Frenkie De Jong, teenage captain Matthijs De Ligt and the Brazilian winger David Neres emerged as stars during the tournament, but there are fears now that the side will be dismantled with bigger clubs willing to sign their best players.
“My thoughts are that we thought Ajax had achieved a certain level of maturity, and they didn’t,” Mourinho said.
“They showed in the second half that there is still naivety in that team, and I think that the philosophy lost against the strategy.
“The philosophy brought Ajax to a disposition of playing fantastically well and arriving with one and a half feet in the final, but then the strategy won.
“We saw many examples in their attacking situations, we had other situations where (Daley) Blind and De Ligt were outside. The basic thing you do when you have an advantage is to keep your balance all the time, never imbalanced.
“The balance starts with the defensive line in position and after that a certain number of players always behind the ball.
“But they stuck with their philosophy, they played the second half like they were playing against Vitesse in the Dutch league.
“They played like it was a group-phase game, or one more game in their own league.”
Louis Van Gaal, another former United manager who guided Ajax to Champions League glory in 1995, was also critical of the way his former club surrendered the initiative against Spurs.
“This defeat was completely unnecessary,” Van Gaal was quoted as saying by Dutch newspaper De Telegraaf.
“At half-time there was nothing wrong with a 2-0 lead.
“In the second half, Tottenham took more and more risks and more and more attackers entered the field.
“Ajax made the wrong choices in possession of the ball in that phase.”
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Petr Cech is adamant Arsenal will keep their feet on the ground in Thursday’s Europa League semi-final second-leg clash with Valencia.
And the veteran goalkeeper insists he is ready for the game despite not playing regularly this season.
The Gunners travel to the Mestalla defending a 3-1 lead from the first leg in north London last week.
Cech, 36, played in that game having been reduced to playing in the Europa League campaign in his final season before his retirement.
The former Chelsea goalkeeper, who could yet face his old side in the Europa League final in Baku on May 29, believes Arsenal will not capitulate having earned a lead heading into the return fixture.
“We keep our feet on the ground and we know that tomorrow is another difficult 90 minutes,” he said.
“We gave ourselves a two-goal cushion, but you know, two goals with the away goals now is an advantage but it’s not a decisive advantage.
“We can see that in the past and we can see it in the future, ties will get overturned with that deficit because football is about that. We respect the opponent and it will be very difficult.”
Cech has had to deal with playing second fiddle to Bernd Leno in Unai Emery’s Premier League side and has been used solely in cup competitions since September.
But, with Arsenal’s hopes of a return to the Champions League now all but resting on winning the Europa League this season, Cech insists he is still raring to go.
“I think the key is in training,” he replied when asked about the difficulty in finding form when you are not playing on a regular basis.
“You keep training at your best and together with my experience, you prepare during the week and even if you play regularly, the key still lies in training.
“If you prepare well then you’ll play well and with all the experience I have, I don’t feel a big difference. I feel prepared for every game.”
Provided by Press Association Sport