The AC Milan striker opened his account early in the first half from the penalty spot before doubling his tally just before half-time, making it 10 goals in his last nine matches for both club and country.
However, the home side could count themselves a little unlucky as they missed a penalty and also clattered the crossbar in the first half.
With Denmark held to a 1-1 draw in Copenhagen by second-placed Bulgaria, Italy extended their lead at the top of their group and even have a game in hand.
Meanwhile, Malta remain rooted to the bottom of the group with zero points from five matches.
Azzurri coach Cesare Prandelli wasn't entirely happy with his side's performance, feeling they should have been more clinical in the final third.
"We knew there wouldn't be space and we were perhaps a little too slow in building up play, so we ran into trouble," he told Rai Sport after the match.
"We still maintained possession throughout the game but lacked a bit of intensity in our finishing."
Midfielder Riccardo Montolivo heaped praise on goal hero Balotelli.
"We tried to keep going through the middle but that was a mistake as they were there waiting for us," he said.
"Malta clammed up and it was difficult to find spaces. Luckily we had that superstar in attack and he sorted it out for us."
The hosts started reasonably brightly, pressing the Azzurri at every opportunity and not allowing them time to settle on the ball. But it was that eagerness to close down at every moment which was soon to be Malta's undoing.
Luke Dimech overstretched as he tried to tackle Stephan El Shaarawy in the eighth minute and tripped the AC Milan forward in the penalty area.
That gave Balotelli the chance to open the scoring, sending goalkeeper Justin Haber the wrong way from the spot.
However, moments later Malta had a penalty of their own as Andrea Barzagli let Andre Schembri race clear into the box only for Gianluigi Buffon to bring him down.
Michael Mifsud stepped up to take the resulting spot-kick but could not beat the Italian number one.
Thirty-one-year-old Mifsud could have made up for that mistake just a couple of minutes later as he left Leonardo Bonucci for dead, but his long-range shot looped over Buffon and smacked the crossbar, much to the disappointment of the Maltese crowd.
Malta then escaped as Riccardo Montolivo steamed forward and rounded Haber, only to see his shot from a tight angle bounce wide.
The Italians slowly started to exert their authority and Andrea Pirlo saw a freekick blocked by the wall, before Balotelli put another just over the bar.
Malta's reprieve was brief, though.
Almost on the stroke of half-time, Bonucci found Mattia De Sciglio on the left with a superb long ball. The youngster showed excellent control as he advanced towards the goal before his cut-back found Balotelli, who side-footed into the far corner from close range.
Italy could, and should, have added another just after the break when Ignazio Abate raced down the right side into the box, but his cross was poorly controlled by Emanuele Giaccherini who, nevertheless, forced a brilliant reflex save from Haber.
Claudio Marchisio was a little fortunate at the other end when he appeared to trip Mifsud as the striker raced into the penalty area, but the referee waved play on, much to the disgust of the Maltese, who were convinced they should have had another spot kick.
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