The hosts, boasting a 100% record in the group going into the game, began brightly against the second-placed Greeks, with Marouane Fellaini heading just wide on the quarter-hour mark.
Michael Skibbe's side held firm come the half-time whistle, before going on to take the lead 20 seconds after the restart
Kostas Mitroglou made the most of a napping Belgium defence to latch on to a Panagiotis Tachtsidis flick-on before sweeping an emphatic half-volley across Thibaut Courtois and into the far corner of the net.
The visitors' evening became more difficult as they fell to 10 men in the 65th minute, Tachtsidis sent off after being shown a second yellow card for a late lunge on Toby Alderweireld.
Boosted by a numerical advantage, Belgium stepped up their attacks, showing more urgency and forcing a number of superb saves from Greece goalkeeper Stefanos Kapino.
As the clock ticked into injury time, the hosts finally succeeded in grabbing an equaliser, Lukaku making up for a tame 89 minutes by chesting Mertens's floated cross from the left, holding off Sokratis Papastathopoulos and rifling a volley on the turn beyond the grasp of Kapino.
Stoppage time brought more drama as the Ethniki stopper kept out another dangerous Lukaku effort, before the visitors lost another player when Georgios Tzavellas was shown a second yellow after a clash with the Toffees marksman.
No more goals were to come, however, as both sides maintained their unbeaten record with four wins and one draw, but Belgium stay on top of the group by virtue of a superior goal difference.