Knowing a win would guarantee them second place in Group G, Porto's nerves were quickly settled when Aboubakar latched on to Yacine Brahimi's through ball after nine minutes.
The powerful striker was in magnificent form, pouncing again in the 33rd minute when he cut in from the left edge of the box and shot beneath Diego Benaglio for his fifth goal of the Champions League campaign.
Monaco, who had lost the 2004 final to the same Portuguese opponents, were reminded of that 3-0 defeat when Aboubakar turned provider, playing in Brahimi for a third just before halftime.
Monaco captain Kamil Glik pulled one back with a 61st-minute penalty, given harshly for a handball from Ivan Marcano, but Porto's Brazilian fullback Alex Telles thundered home a 25-metre shot four minutes later.
Radamel Falcao nodded in a 78th-minute consolation against his old club before Tiquinho Soares struck again with another header for the home side with just two minutes remaining.
The victory took Porto to 10 points behind group winners Besiktas, who moved on to 14 after their 2-1 win at RB Leipzig ensured the German newcomers missed out in third place on seven points.
For Monaco, though, the conclusive defeat only demonstrated how far they have fallen since their exciting young side was broken up after reaching the semi-finals last season.
For the prolific Falcao, still Monaco's brightest spark in a dismal season, it was a bittersweet return to the Dragao, where he won six trophies with Porto.
"For me, it was a huge pleasure to come here and play again. It's like my home and I won a lot of trophies here," the Colombian told UEFA.com.
"Now we have to focus on the league and the two domestic cups. It's sad not to be continuing in the Champions League but that's football.
"Our team changed a lot in the summer and we need time to get stronger. We are capable of finishing second in the league in order to return to this competition."
(Reporting by Ian Chadband, editing by Ed Osmond and Toby Davis)
