The Milan striker netted twice in the first half to power the Azzurri past a stubborn Malta side that gave the Italians plenty to worry about in this intense encounter.
The win gives Italy a three-point lead over Bulgaria with a game in hand in Group B.
Balotelli gave the visitors a dream start in the seventh minute when he coolly slotted a penalty past goalkeeper Justin Haber after Stephan El Shaarawy was taken down in the box.
The hosts were a goal down but clearly not rattled as they won a penalty of their own in the 16th minute. However, Michael Mifsud could only watch in disbelief as Gigi Buffon did ever so well to keep his drive out of the net.
Mifsud had another glorious opportunity to level matters, but his well-struck shot from distance crashed off the crossbar.
Balotelli then struck the decisive blow on the cusp of half-time as he volleyed past Haber to give the Italians a 2-0 lead heading into the interval.
Malta had a couple of good opportunities to claws its way back into the match in the second half but the visitors defended well and secured all three points.
Italy coach Cesare Prandelli praised Malta’s resistance but said that in the end his team’s quality ruled the day.
“We have to treasure the fact that when we come up against a well-organized team, we have to be quicker with our play,” he said. “But the great performance against Brazil and the three points tonight are paramount.”
Mario Balotelli’s two goals now give him nine in 10 appearances for club and country since his winter transfer from English club Manchester City.