Having missed the first leg, Diego Costa has continued his fine goalscoring form against the Gunners.
A quiet first half at the Estadio Wanda Metropolitano was punctuated by a breakthrough from the former Chelsea man in added time of the first half.
A fine ball from Antoine Greizmann found the path of the Spaniard, who bullied Arsenal full back Hector Bellerin, holding him off long enough to put the ball past David Ospina, who dived pretty early for the shot.
The strike is Costa’s fourth goal against Arsenal in seven games.
Atletico now lead 2-1 on aggregate, though the goal doesn’t change the fact that Arsenal need a goal of their own tonight regardless, by virtue of Greizmann’s away goal at the Emirates last week.
Arsenal captain Laurent Koscielny was forced off in the first half with an unfortunate torn achilles tendon which is set to rule him out of the World Cup for France.