The win means Belgium are also set to rise to number one in FIFA's volatile ranking system, while Israel's hopes of reaching the tournament in France next year were ended.
Belgium had already qualified after a 4-1 victory over Andorra on Saturday and Tuesday's win kept them two points clear of Wales in the standings.
Belgium had the lion's share of possession throughout the match and would have been ahead at halftime but for a spectacular miss from Mertens. Faced with an open goal some two metres out, he somehow shot wide.
In the 64th minute, however, he made amends, taking a pass from Kevin De Bruyne and shifting right to bypass the defence and drive low past Israel keeper Ofir Marciano.
De Bruyne's dipping and bouncing free kick was also too much for Marciano in the 78th minute and Mertens was on hand again six minutes later to find an unmarked Eden Hazard in front of goal, for an easy finish.
Israel, who came into the match with a chance of overhauling Bosnia in third, came close midway through the first half when Eran Zahavi curled a free kick against the post. Tomer Hemed's headed goal for Israel in the 88th minute was simply a consolation.
(Reporting By Philip Blenkinsop; editing by Toby Davis)
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