The Napoli man buried Nacer Chadli's pass against the 10-man visitors after the game had been suspended due to torrential hail in the first half
Dries Mertens' goal a minute from time handed the hosts a win in their final friendly ahead of the World Cup in what was otherwise a disjointed Belgium performance probably not helped by the stoppage.
Heavy rain began to fall as soon as the two sides kicked off in Brussels, and that soon turned to hail as the game progressed.
With 23 minutes gone, Hungarian referee Viktor Kassai called a halt to proceedings as Kevin Mirallas prepared to take a right-wing corner for the hosts.
It seemed the correct decision, with hail stones the size of golf balls beginning to bounce off the turf, and the two sets of players retreated to the dressing rooms to wait for the storm to abate.
When play resumed, a turgid encounter unfolded, with the visitors reduced to 10 men midway through the second period as Issam Jemaa was shown what appeared to be a harsh second caution, seemingly for an attempted handball.
Despite the man advantage, Belgium toiled to make the breakthrough in the remaining 25 minutes, but Mertens' late strike at least ensures they will depart for Brazil on a winning note.
Mirallas brought the first real save out of either goalkeeper in the 11th minute, thumping a 30-yard free kick in on goal which Farouk Ben Mustapha punched away to safety.
Divock Origi, selected by coach Marc Wilmots in the loan striker role ahead of Romelu Lukaku, brought another save out of the keeper three minutes later after a sharp turn in the box, but once again Ben Mustapha was equal to the effort.
Following the lengthy weather delay, the hosts lost their early momentum and struggled to create chances against a stubborn Tunisia defence.
On the one occasion they did break through prior to the interval, four minutes before the break, Mirallas dragged his low effort narrowly wide of the right-hand post after running onto Eden Hazard's beautifully weighted pass.
Following a low-key start to the second half, Jemaa was given his marching orders by Kassai after being shown two yellow cards.
Already shown a caution for a first-half tangle with Jan Vertonghen, the attacker was sent from the field after trying to control a long ball under pressure from Vincent Kompany - remonstrating furiously with the referee on his way off the pitch.
Tunisia made light of their disadvantage and almost took the lead shortly afterwards, Syam Ben Youssef heading Yassin Mikari's left-wing free kick over the crossbar.
Vertonghen then fired a 79th-minute free kick narrowly wide of the post as Belgium pressed for a late winner, which duly arrived in the 89th minute, Mertens evading the attentions of two players and slotting home after being picked out by Nacer Chadli's pass.