The hosts have secured second place in Group G, finishing as runners-up to Besiktas, while Monaco could not do enough to qualify for the Europa League as they finished last in the standings.
The French outfit have suffered a fall from grace since allowing the likes of Kylian Mbappe and Bernardo Silva to leave the club in the summer as they conceded 16 goals in the Champions League group stage this season.
Aboukabar came close to nabbing another goal a few minutes later when he was picked out in the box, but his close-range effort soared over the crossbar.
Porto created wave upon wave of attack as Danilo Pereira unleashed a thumping hit from the edge of the box, with the ball aiming towards the bottom left corner of the net, but the goalkeeper managed to stop its path.
The hosts doubled their lead just after the half-hour mark when Pereira found Aboubakar in the middle of the danger area and the striker slotted home with a low shot.
There was controversy in the 39th minute when both teams went down to 10 men as a result of Rachid Ghezzal and Felipe getting sent off after coming to blows on the pitch.
At the other end, Brahimi nabbed the team's third goal of the night by charging away from his marker and beating the keeper one on one.
Monaco managed to score a second in the closing stages of the match when Radamel Falcao headed home from close range, but it was not enough to launch a serious comeback as Porto had earlier nabbed a fourth when Alex Telles delivered the ball into the bottom corner.
In the end, Tiquinho Soares wrapped up the contest by scoring a header from inside the box after latching onto Pereira Ricardo's cross.