Atletico had not scored in this season's Champions League, including a 4-0 drubbing at Chelsea last month, but went ahead after 66 minutes thanks to a spectacular strike from Aguero.
Aguero, who had replaced the ineffective Florent Sinama Pongolle after 54 minutes, capped a fine performance with a curling free kick to level for Atletico in the final minute.
Porto's 1-0 win at APOEL Nicosia meant the Portuguese team and Group D leaders Chelsea both went through.
Atletico, third with two points from four games, can still claim a spot in the Europa League.
Atletico Madrid's Sergio Aguero celebrates after scoring his second goal
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