The two teams played out a 2-2 draw at Vicente Calderon, and the Spanish outfit had to score away to salvage qualification for the next round.
The home side were lucky to escape a penalty on 26 minutes after Simao was clearly brought down in the area by Bruno Alves.
Atletico keeper Leo Franco did well to save a powerful volley from Fernando eight minutes later.
Franco was alert once again to deny Porto, after the Argentine guardian made a terrific dive to save Rodriguez's header mid-way through the second-half.
Porto striker Hulk had another golden opportunity wasted after he saw his shot rattle Franco's bar in the 78th minute.
The game's best chance fell to Porto's Lisandro Lopez, who successfully rounded Franco before hitting the post from a tight angle.
Atletico seemed out of sorts as the game neared its end, and the goalless draw was enough to earn Porto a place in the Champions League next round.