It was a dramatic end to a stage which had been stopped at one point as riders were affected by a spray used by police to break up a farmers’ protest on the road from Carcassonne.
Mitchelton-Scott’s Yates led on the descent into Bagneres-de-Luchon after attacking three kilometres before the summit of the Col du Portillon, cresting the mountain with a 22-second advantage.
But the 25-year-old Lancastrian crashed with 6.5km to go, allowing Quick-Step Floors’ Alaphilippe to zip by and take his second stage win of this Tour.
Yates was quickly back on his bike, and followed home Bahrain-Merida’s Gorka Izagirre to finish third.
The main contenders crossed the line in a group some nine minutes after Alaphilippe to mean there is no change at the top of the General Classification.
Team Sky’s Geraint Thomas continues to lead by one minute and 39 seconds from team-mate Chris Froome, with Team Sunweb’s Tom Dumoulin a further 11 seconds behind.
Several riders, including Thomas and Froome, needed treatment after being affected by what was thought to be tear gas used by police to break up a farmers’ protest early in the stage.
The protestors had rolled large hay bales into the road 29 kilometres into the 218km stage, and then clashed with police who tried to remove them.
After a spray was used by officers, it appeared to get into the eyes of several riders, with world champion Peter Sagan also among those affected.
The race was stopped completely while they received medical attention and washed their eyes. After a 15-minute interval the race resumed with a short neutralised section before the flag was dropped once again 33km into the stage.
Farmers’ protests are nothing new at the Tour, but the incident will add to the intense security situation in this year’s edition.
Froome was jostled and spat at on Alpe d’Huez, while 2014 winner Vincenzo Nibali saw his race ended after he was brought down in a tangle with a fan on the same mountain.
Former world champion Philippe Gilbert, meanwhile, got back on his bike to continue Stage 16 despite a spectacular crash that sent him flying over a wall.
Gilbert, a Quick-Step colleague of Alaphilippe, was 57.2km from the finish and in the lead of the race when disaster struck.
Negotiating a left-hand bend at speed, the Belgian failed to brake in time, skidded and was sent flying head first over a parapet and into a ditch.
The former Tour of Flanders and Liege-Bastogne-Liege winner was helped back up on to the road and given first aid before resuming the stage in the company of a group of frontrunners.
Although shaken, the 36-year-old looked to have suffered only bruises and scratches.
Medical services which are on hand throughout the race attended to Gilbert’s injuries as he rode alongside the doctor’s car.
After a delay in proceedings thanks to a protest by farmers, the 16th stage of the Tour de France got underway on Tuesday.
Tear gas was used to break up the gathering as farmers demonstrated against a cut in state aid.
Team Sky’s overall leader Geraint Thomas was among the riders affected by the tear gas and was seen rubbing his nose following the incident.
A video footage that emerged after the sequence of events showed liquid being blown back into the advancing peloton after being sprayed by an officer from France’s national gendarmerie.
Apparently, Tour de France medical officers did hand out eye drops to riders including green jersey points leader Peter Sagan.
The 218km stage which ends in Bagneres-de-Luchon restarted at 12:36 (10:36 GMT) after an interruption that lasted around 15 minutes.
“After a 15 minute-long interruption caused by protesters, the race is back on,” organisers said in a brief statement on leTour.fr.
Team Sky principal Sir Dave Brailsford took aim at Tour de France spectators who have jostled and spat at his riders this week, asking if they would rather have a race purely for French teams if they do not respect the world’s best cyclists.
It is nothing new for Sky to face hostility in France, but the atmosphere has been even darker this year in the wake of Chris Froome‘s salbutamol case, in which he was cleared of wrongdoing just days before the Tour began.
That verdict has not been accepted by many fans, not to mention significant elements of the French media, and contributed to scenes which saw Froome slapped and spat at on Alpe d’Huez, and doused with an unidentified liquid on Saturday’s stage to Mende.
Brailsford said he could not understand why the team only get this reaction in France, given Froome rode and won the Giro d’Italia in May while his case was still open.
“It just seems to be a French thing,” he said. “Like a French cultural thing. I’m not sure they’d have liked their football players being spat at in Russia (at the World Cup). I’m sure there would have been a word or two about that.
“But it’s OK to spit on us and on our staff… The Tour de France is promoted as the world’s greatest annual sporting event and, if you want the best international riders to come to your country, maybe treat them with a little more respect.
“If you don’t want them to come, you can maybe have the Tour de France for French teams – that might work – but if you want international teams to come then maybe treat them with the same respect that you’d want for your team.”
Sky have dominated the Tour in recent years, winning every edition since 2012 bar the 2014 race in which Froome crashed out on stage five.
The reaction they have received is not unique, and French fans have often turned against serial winners, whether it be Eddy Merckx or even their own Jacques Anquetil and Bernard Hinault.
While incidents of actual violence – such as the fan that slapped Froome on Alpe d’Huez – are of concern, Brailsford said Sky had learned to tune out the boos.
“I don’t think it’s going to stop,” he said. “I’m not too optimistic on that front. We accept it and we have to make a decision about how to behave. We’re trying to remain dignified, we’re trying not to react and we’re trying not to get distracted by it.”
Sky’s bid to ‘remain dignified’ was not helped by one of their own over the weekend, when Italian rider Gianni Moscon was disqualified from the race for striking Frenchman Elie Gesbert of Fortuneo-Samsic just 800 metres into Sunday’s stage.
“I don’t know how people are going to react, but it’s not going to calm people down,” Brailsford said.
It is just the latest incident in a long line of disciplinary mis-steps from Moscon, who was suspended for six weeks last year after racially abusing fellow rider Kevin Reza.
Brailsford said he would consider if Moscon should face further punishment after the Tour, but, when asked directly, would not rule out terminating the 24-year-old’s contract.
“Obviously Gianni has left the race, which is very disappointing,” Brailsford said. “He’s really disappointed. He’s let himself down, he’s let his team down and now he’s gone home.
“From a team point of view, I’m going to keep the focus on the rest of this race here, and then next week I will gather the facts, look at the process and go from there.”