The in-form AC Milan striker slotted home a penalty before notching again just before halftime, as the Azzurri overcame their upstart opponent.
The enigmatic forward opened the scoring from the spot just seven minutes in after AC Milan teammate Stephan El Shaarawy had been sent tumbling in the area.
Malta could have responded in kind, but Michael Mifsud saw his penalty well saved by Gianluigi Buffon, who had felled Andre Schembri in the area, and it proved a costly miss as Balotelli struck again right on the stroke of halftime to break the hosts' game resistance.
Malta had gone into the game without a home win in a competitive international for seven years, but for long stretches of a low-quality encounter it looked in no way inferior to a side positioned 142 places higher in the FIFA rankings, with Mifsud looking particularly menacing up front early on.
It was Italy that opened the scoring, though, with Balotelli slotting home from the spot in characteristically cool fashion, after Luke Dimech had clumsily upended El Shaarawy just inside the area.
Italy’s all-Milan frontline very nearly combined for a second goal just moments later. El Shaarawy whipped a shot just wide after being put into space by a back-heeled lay-off from Balotelli.
Malta should have levelled matters 16 minutes in when Buffon took Schembri down as the attacker tried to round the Juventus shot-stopper. The Azzurri skipper avoided a red card as Schembri had been going away from the goal, and that proved crucial, with Buffon making amends for his error by parrying Mifsud’s well-struck but poorly directed spot-kick away to safety.
While Malta’s record goalscorer only had himself to blame for failing to convert from 12 yards out, he was desperately unfortunate to see a thunderous long-range effort crash against the crossbar with Buffon beaten.
Riccardo Montolivo then went close for Italy, lofting the ball onto the roof of the net after taking an El Shaarawy cross in his stride, but Malta proved to be incredibly game for the challenge, and Clayton Failla called Buffon into action once more with a long-range free kick.
The hosts were rocked by the concession of a second goal right on the stroke of halftime that underlined the clear gulf in class in terms of finishing. Leonardo Bonucci played a sublime ball over the top that Mattia De Sciglio killed wonderfully well before laying the ball off for the supporting Balotelli, who calmly placed the ball past Justin Haber and into the far right corner.