Goals from the 20-year-old and Roque Santa Cruz sealed the win for the Andalusians, and the former Lyon midfielder was full of praise for the Spaniard after the match, suggesting he is Malaga's version of Barcelona star Lionel Messi.
“Those games, you have to have great players to unlock them. Barcelona have Messi, we have Isco," he told reporters.
"This is historic. Since the beginning of our adventure, we have tried to go the furthest possible. We had to qualify. We played to our strengths."
Isco opened the scoring in the first half with a terrific strike into the top corner, and could barely hide his disbelief at just how far the side have come in Europe this season.
“It's a dream,” he said, “Something we could never have imagined in this city. We deserve it. When we got going, we enjoyed our football again, which is our thing."
This is the Spanish outfit's maiden adventure in the Champions League, and the Spain Under-21 international conceded he is simply happy to still be involved in the competition.
He added: “The important thing is that we are still in the Champions League, which is the essence of football."
The match was on a knife edge for the majority of the second half as Isco's opener had cancelled out Joao Moutinho's solitary strike from the first leg.
It looked to be destined for extra time at La Rosaleda, until Santa Cruz came on with 15 minutes to go to glance a header home and send the home support into raptures.
The Paraguayan was also elated with the win, telling reporters: “We are all so happy and now we must enjoy what we have achieved here. I am happy to have scored and because of the fact that we won.
“This group of players and the fans deserved it. The friendship and closeness within the squad is fundamental.”
Malaga now find themselves in the draw for the quarter-finals of the Champions League, which takes place on Friday, March 15.