Colombian forward Radamel Falcao scored a classy back-heeled goal in the 75th minute to tilt a match which seemed headed for a draw as neither a lethargic Porto nor a struggling Atletico looked like scoring.
Missing influential midfielder Fernando through suspension, Porto could not keep possession to create a high enough tempo in the first half.
Their only clear chance came in the 11th minute when Meireles's first-time shot in the box was blocked by Ujfalusi.
Atletico rarely threatened either and their best chance came through a Porto error, Aguero pouncing on Tomas Costa's back pass but directing his powerful shot straight at Helton.
Porto coach Jesualdo Ferreira said the midfielder's introduction may have been the key to the win.
"The way Atletico played, with four central defenders, didn't allow us to play quickly, there was never space. Guarin's entrance freed space for Meireles to widen the game and serve Hulk.
"That gave us the goal and allowed us to keep control," Ferreira said.
Five minutes later, Porto's central defenders went up for a corner and created the second goal. Bruno Alves's crashing header hit the post but the rebound fell to his defensive partner Rolando for an easy tap-in.
