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.
The Spanish side have yet to win a match in La Liga this season but their forward players linked up well for much of the match.
On 52 minutes that almost paid off when a fluid move led to an Ujfalusi shot which forced Helton into a good save.
Substitute Freddy Guarin almost made an immediate impact for Porto when his 67th minute shot was blocked by David De Gea.
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.
De Gea, a 19 year-old who replaced the injured Roberto in the first half, made a reflex save from a Hulk shot in the 75th minute but the ball fell back to the Brazilian striker who slipped it through for Falcao to backheel into the net.
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.
