The result leaves the Portuguese giants at the top of Group G, ahead of Premier League champions Chelsea and on course to reach the knockout stages.
In the process manager Julen Lopetegui recorded his twentieth consecutive home win, one more than José Mourinho managed whilst at FC Porto.
The all-time record of twenty-four consecutive home wins is held by Artur Jorge, some thirty years ago.
Vincent Aboubakar opened the scoring for the Dragons midway through the first-half and Yacine Brahimi doubled the lead just before the break.
Maccabi failed to record a shot on target until the 87th minute and are still waiting for their first goal after three matches in this season’s tournament.
The visitors were off-target with six long-range efforts in the opening half-hour, while Tal Ben Haim II, there are two players with identical names in the Macabbi team, felt he should have had a penalty when tripped by Martins Indi as he prepared to shoot.
The referee adjudged the Dutchman had got a toe to the ball and turned away the vehement appeals.
Aboubakar broke the deadlock when Layun whipped over a stunning cross from the left and the Cameroon striker’s diving header had too much power for Rajkovic.
Aboubakar turned provider four minutes later when he slipped a pass through to Brahimi who calmly slotted the ball home. Porto nearly made it three when Cristian Tello squared the ball towards Aboubakar, but Tal Ben Haim I, was fortunate to see his interception cannon off the crossbar.
FC Porto’s Martins Indi then missed a great chance when Ruben Neves, the 18-year-old making Champions League history as the youngest-ever captain in the competition, laid on a perfect pass for the defender who somehow managed to skew his shot wide with the goal gaping.
Another record breaker on the night was keeper Iker Casillas who has now kept fifty-one clean sheets in the competition during his time at Real Madrid and now at FC Porto.