Defender Nacho, who had been out since the start of April with a thigh problem, also took part in the light session a day after Real beat Leganes in La Liga.
Isco injured a shoulder in the first leg in Munich last Wednesday. On Friday, coach Zinedine Zidane said that the player would be out of the return leg on Tuesday.
“There is nothing we can do, that is how it is,” Zidane said.
While Spanish media suggested that Isco could play with a pain-killing injection, Zidane insisted that he would not take risks with players who were not 100 per cent. Real lead the tie, 2-1.
While Zidane said on Saturday that picking Nacho would be “complicated”, his return could offset the loss of Dani Carvajal who suffered a thigh injury in the first leg.
The defending champions, who could add sparkle to what has been a difficult season by winning their third consecutive Champions League crown come what May, have struggled for consistently domestically this term and are fighting to cling onto third place with Valencia in hot pursuit.
“We can’t be happy with what we’ve done in the league in general. We lost a lot of points at the beginning, then we were a bit better but that can happen in a season,” Zidane said post-match at the Bernabeu.
“Now we have to get back to work, we have another match on Tuesday which will be our game of the year. We have a title to defend.”
Gareth Bale could yet stay at Real Madrid beyond this season, with reports suggesting no other team will be able to stump up at least £60m, Los Blancos’ rumoured asking price, to land the out-of-favour attacker in the summer.
According to The Express, the Welshman is set to be priced out of a move with the Whites being determined to command back a high fraction of the £80m fee they shelled out in 2013.
Indeed, the 28-year-old is also on a £18m-a-year contract at the Bernabeu, which runs until 2022 – terms few other teams could match.
A return to Tottenham has been touted while Manchester United have also been long-time admirers of the three-time Champions League winner – but it remains to be seen whether either of those Premier League outfits would be prepared to play such a large sum for a player who turns 29 in July.