Los Boquerones booked a place in the Champions League quarter-finals with a goal either side of half-time as the Dragoes relinquished their first-leg lead in Spain
The Andalusians suffered their first ever defeat in European competition in the first leg but a sublime goal from Isco levelled the tie at half-time. The hosts dominated the second half as Steven Defour was shown a red card in the 49th minute and Roque Santa Cruz finally secured the win with a header 13 minutes from time.
There was very little to separate the two teams at the Dragao three weeks ago and it was clear the return leg would follow suit within 10 minutes of kick off, but neither Joaquin or Danilo managed to test the opposing keeper from decent positions.
The game continued at a largely tentative pace, with neither side showing any urgency to make the tie swing in their favour.
The tackles were heated and quality was in short supply but in the 36th minute Helton, who had largely remained untested until this point, produced a great save to keep Antunes' arrowed shot out of the top corner.
It was the start of a good spell for los Boquerones, and they thought they had taken the lead through Javier Saviola in the 39th minute. However, the goal was ruled out due to a collision between Julio Baptista and Helton, though the former Arsenal forward looked to have been pushed into the keeper.
But Malaga did not have much longer to wait for a moment to cheer as Isco scored a sensational goal. The Spaniard was afforded too much space 20 yards from goal and he used it to devastating effect as he clipped a brilliant cross-goal shot into the far corner.
The Dragoes' hopes of progression took a severe blow early in the second half as Defour picked up his second yellow card for an idiotic challenge on Joaquin.
Malaga did not rush to find a second goal, and it was not until the 57th minute that they came close again. Isco's cross was sent straight to Saviola following a poor clearance from Nicolas Otamendi, but the centre-back got across to block his compatriot's effort on goal.
Four minutes later Isco came close to grabbing his second as he connected with a smart pass from Saviola. Helton rushed out to him and from an acute angle he could not roll the ball into the net
Manuel Pellegrini's men allowed the game to go stale and were almost punished as a result: Jackson Martinez was agonisingly close to converting James Rodriguez's free kick 15 minutes from time.
The Andalusians heeded their warning and found the decisive second goal three minutes later as Santa Cruz rose highest to head in from Isco's corner.
Porto did get the ball in the back of the net moments later through Maicon, but the goal was correctly ruled out for offside.
It proved to be their final chance to remain in the competition and Malaga ended a run of four games without a win to book their spot in the quarter-finals in their maiden Champions League campaign.