The Spanish outfit entered the match trailing 1-0 from the first leg, but Isco levelled the tie at 1-1 with a curling effort in the latter stages of the first half.
The match looked set for extra time as the final 10 minutes approached, but Roque Santa Cruz sent Malaga into the quarter-finals with a header from an Isco corner after 77 minutes.
Here Sports Mole dissects the 90 minutes of action between the two European rivals.
On target: 5
On target: 1
Was the result fair?
There is no question that Malaga deserved to book their spot in the quarter-finals this evening. Porto were perhaps the better side in the opening 25 minutes, but the Spanish outfit did not look back after taking the lead on the night through Isco. The expected onslaught from Porto in the latter stages just never arrived.
The La Liga outfit can be proud of their performance this evening. They were much the better team against a side that has not lost a domestic match this season, while Manuel Pellegrini was prepared to throw on attacking players to go for the win in the latter stages rather than settle for extra time. They will not be in the competition next season, but they will give it their all in this campaign.
Porto were really disappointing this evening. They started the match with a high tempo, but seemed to lose their way when Joao Moutinho was forced off at the interval. The red card certainly did not aid their cause, but they didn't offer anywhere near enough in attack to be worthy of a spot in the last eight. The statistic of one shot on target tells its own story.
Sports Mole's man of the match
Joaquin: The electric pace may have gone, but the Spaniard still has that football brain. He was just sensational this evening as he dictated the tempo for an hour of the match, before understandably tiring in the latter stages. He was everything that his team needed him to be.
Having already been booked in the first period, Defour decided to dive into a challenge with Joaquin in the early stages of the second half. The referee simply had no option but to send him from the field. It left his side with a mountain to climb.
Nicola Rizzoli had a productive 90 minutes of action this evening. He was forced into a number of decisions in the first period, but was correct more often than not. He also rightly dismissed Defour in the early stages of the second half. However, Malaga were unhappy with his decision to chalk off a Javier Saviola 'goal' in the first period.
Malaga: Malaga will attempt to consolidate fourth position in La Liga when they host Espanyol on Sunday.
Porto: The Portuguese outfit return to domestic action away to Maritimo on Sunday.