Coach Roberto Martinez's men also struck through Thomas Meunier, Eden Hazard, Yannick Carrasco and an own goal from Ragnar Klavan, with the first three coming inside the opening 25 minutes.
Estonia replied just before the half-hour through Henri Anier but it was a lonely highlight for the Baltic nation who are second from bottom with three points.
Meunier's first international goal after eight minutes began the deluge as he timed a run to the back post perfectly to head home Carrasco's cross.
Mertens' shot from outside the area took a wicked deflection for the second goal after 16 minutes and Hazard made it 3-0 with a powerful drive after a swift attacking move.
A rare defensive slip then allowed Anier to turn and beat keeper Thibaut Courtois before the break.
Belgium added three more goals in six minutes soon after the hour mark as they claimed their fourth group victory.
Unmarked Carrasco finished off a square pass from Lukaku before Klavan steered a centre by Mertens into his own net.
Mertens then grabbed his second goal with a chip over the goalkeeper after Lukaku's effort had been well saved.
Lukaku was rewarded for his contribution when his 83rd- minute shot took a deflection to leave goalkeeper Mihkel Aksalu with no chance.
The Everton striker was then fed five minutes later with a clever ball from midfield and he raced towards goal before shooting into the corner of the net.
Belgium have 12 points from four games, two ahead of second-placed Greece and five in front of Bosnia who are third.
Greece were held 1-1 at home by Bosnia on Sunday.
(Reporting by Mark Gleeson; Editing by Tony Jimenez; mark.gleeson@thomsonreuters.com; +27828257807; Reuters Messaging: Reuters Messaging: mark.gleeson.thomsonreuters.com@reuters.net)
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