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The Republic of Ireland now need Greece to beat the Belgians by a single goal in Brussels on Tuesday if they are to progress now to the play-offs - and land a place in next year's finals.
Don Givens had retained the same 11 after the 2-0 win over Greece two weeks ago.
Martens had the game's first real chance in the 12th minute but he headed over from close range after connecting with a cross from the right from Tom De Mol.
Michael Timlin was playing in front of his watching club manager Chris Coleman and he came close for the Irish with a powerful strike in the 24th minute.
Sheffield Wednesday midfielder Glenn Whelan was unlucky to see a blistering strike from just outside the box fly over in the 36th minute.
Whelan then created a brilliant chance for Stephen Ward two minutes later but after the Bohemians striker rounded goalkeeper Michael Cordier but his shot trickled wide at the near post.
Former Tottenham midfielder Jonathan Blondel almost silenced the home crowd 60 seconds later with a blast which flashed across goal from just outside the box.
Blondel had a vital role in Belgium's winner when he squared for substitute Jeanvion Yulu-Matondo to shoot goalwards from six yards out.
Paul Keegan made a brave block but the ball fell perfectly for Martens to slam past Colin Doyle from 10 yards out.
Belgium's back four proved too tight for the Irish to find any way through and they seldom seemed stretched.
Ward could not connect with a knock-down by Kevin Deery in the 64th minute after good work by Willo Flood on the left wing.
Martens should have picked up a second goal in injury-time but he shot wide of an empty net after he had rounded goalkeeper Doyle.
A tense game produced a string of yellow cards for both sides and the Irish will face an anxious wait to see if they will remain in the competition.