Italy strengthened their grip on top spot by moving onto 13 points from five qualifiers while Malta, who slumped to a heavy 6-0 defeat by Bulgaria in Sofia last Friday, remain bottom with no points from five outings.
Buoyed by his outstanding goal in the 2-2 friendly with Brazil on Thursday, Balotelli again delivered the goods for Italy who survived two scares in the first half before applying the killer blow with a second goal in the dying minutes of the opening half.
"We have to treasure the fact that when we come up against a well-organised team we have to be quicker with our play," Italy coach Cesare Prandelli said.
"We were well prepared for the match... I urged the players to approach the match with the right attitude.
"The great performance against Brazil and the three points tonight are paramount."
Spot-kick specialist Balotelli gave Italy a sixth-minute lead with a well-taken penalty after Malta defender Luke Dimech floored Stephan El Shaarawy in the penalty area.
Despite conceding so early in the game, Malta refused to lie down.
Their bold reaction unsettled Prandelli's men whose struggles were laid bare when, on 16 minutes, goalkeeper Gianluigi Buffon brought down Malta midfielder Andre Schembri in the box after an intelligent pass from Roderick Briffa.
Michael Mifsud marched towards the spot but his low effort was stopped by Buffon.
The Malta captain threatened to make amends in spectacular fashion minutes later when he sped past Leonardo Bonucci but his screamer from distance cannoned off the crossbar after taking a slight deflection off Andrea Barzagli.
With the lively Schembri shadowing Andrea Pirlo, Italy's midfield schemer, and all the Malta players pressing hard all over the pitch, Italy were knocked off their stride as the hosts, spurred on by 17,000 fans, pressed for an equaliser.
Italy made the hosts pay for their missed opportunities though as Balotelli volleyed past Malta goalkeeper Justin Haber on the stroke of half-time after a surging run by right-back Mattia De Sciglio.
The second half was less eventful as Italy seemed content to keep possession and protect their two-goal lead with Malta only going close twice through Alex Muscat and Mifsud.
The game ended in the same scoreline as the September match in Italy.
Malta coach Pietro Ghedin was pleased with his team's much-improved showing after the dismal outing against Bulgaria.
"I am very pleased with the performance, especially after last week's disappointment against Bulgaria, but I'm upset that we missed some good chances," Ghedin, who is in his second spell at the helm of Malta, said.
"It would have been better if Mifsud had converted the penalty but he is a very hard-working player, who has 36 goals for Malta and is part of the country's football history."
After the match Italy reserve goalkeeper Morgan De Sanctis of Napoli, 36 on Tuesday, announced he was quitting internationals.
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