The Gunners came from 2-0 down to draw the second leg of their quarter-final at CSKA Moscow 2-2 on Thursday night, progressing 6-3 on aggregate against the Russian side.
The other semi-final will be between French club Marseille and Austrian outfit Salzburg, who advanced following fine comeback wins over RB Leipzig and Lazio respectively.
The first legs will be played on April 26, when Arsenal will be at home, with the second legs on May 3.
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Atletico, who dropped down from the Champions League following the group stage, progressed at the expense of Sporting Lisbon, despite a 1-0 defeat in Portugal on Thursday evening.
Diego Simeone’s side are currently second in LaLiga behind runaway leaders Barcelona.
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.
“Looking at all the results as a whole picture in Europe this week, you would say that teams have become closer and the games are very open and everything is possible in every single game,” Wenger said.
“Everybody speaks about Atletico Madrid that they look the strongest team on paper, but you must say when you look at the results that Salzburg have done again…
“I am from France and Marseille are in there as well and that is always a difficult place to go… maybe it is better that I don’t wish for anybody.”
Arsenal goalkeeper Petr Cech believes winning the Europa League would be a sign of progression for the Gunners this season, following an otherwise indifferent domestic campaign.
The Europa League is Arsenal’s only remaining chance of silverware this season and their most realistic route back into the Champions League as the Gunners are 13 points adrift of the Premier League top four.
“You need to keep the progression. You keep that not only on the pitch, but by winning things,” Cech, who lifted the Europa League with Chelsea in 2013, replied when asked what winning a European trophy does for a team.
“Obviously it will be very important for the club to finish the season with a European success and most importantly, if we can book the spot in the Champions League for next season.
“We know this is our chance to book our Champions League spot but not only that, you play a European competition for a cup and for a cup the club has never won.
“This is another opportunity to add a great trophy to the cabinet.”