The Gunners are now sixth in the Premier League with little prospect of finishing in the top four and taking one of the Champions League qualification spots.
Speaking after Thursday's match in Moscow, when at one point Arsenal had been a goal away from elimination, manager Arsene Wenger admitted he would prefer to avoid Atletico.
The Gunners will know that they can not afford any more wobbles if they are to emerge victorious, with Atletico set to provide a stern test of their credentials.
The Spain striker was often Arsenal's bogeyman during his time at Chelsea...
The final is in Lyon, France on Wednesday, 16 May, with the victor guaranteed a spot in next season's Champions League.
In the other draw, Marseille will face Salzburg.
A European club record 58,897 turned out to roar them home in the second leg against Leipzig on Thursday.
Atletico progressed at the expense of Sporting Lisbon, despite a 1-0 defeat in Portugal on Thursday evening.