The inspirational midfielder's goal early in the second half inflicted the Andalusians first defeat of the competition and put Vitor Pereira's side in the driving seat
In what was a largely stale first half, Manuel Pellegrini's selection of two immobile strikers in Julio Baptista and Roque Santa Cruz saw his side pose very little threat as the hosts dominated possession. However, it was not until the second half that Vitor Pereira's men made their superiority on the night count as Joao Moutinho slotted home a tidy finish to win it.
The Dragoes started brightly as Marat Izmailov shifted the ball onto his right foot in the third minute but was unable pick out the bottom corner of Willy Caballero's goal.
Things did not continue at quite the same pace, but the hosts still looked like the more threatening side in a cagey affair, particularly from set pieces. In the 20th minute Silvestre Valera flicked on a corner from the near post which narrowly evaded Fernando for a simple finish.
Malaga were finding it difficult to create anything in the opposition half, with Isco not seeing enough of the ball to weave his magic in the opening half hour.
Conversely, Jackson Martinez was looking a real handful down the other end. He displayed a knack for running into space behind the defence but Malaga worked well as a unit to ensure he was not allowed too much freedom.
The Andalusians only managed a single shot on goal in the first half and a similar pattern followed after the break. Again it was Izmailov who was the danger, but after eluding Antunes he failed to divert Valera's cross on target from close range.
Jeremy Toulalan then got in a vital block to deny Lucho Gonzalez but it did not take much longer for the Dragoes to find the net.
Alex Sandro split the defence with a fantastic low pass from the left and Moutinho, who waltzed into the area between the centre-backs, guided the ball through the legs of Caballero with a first-time finish after 56 minutes.
The goal forced Malaga into rethinking their plan of attack, but the Portuguese outfit were unwilling to relinquish possession to their opponents.
James Rodriguez ensured things remained on an upward trend following the goal after coming on from the bench but that soon wavered as the Spaniards offered very little in response.
Pellegrini's changes failed to bring his side to life as Porto cruised to a comfortable win which was just their 13th victory in 38 meetings with teams from their neighbouring country. Malaga will welcome the Portuguese side to La Roselada on March 13 with the onus firmly on them to seize the initiative.