The AC Milan striker has now scored 10 goals in nine appearances for club and country since leaving Manchester City in January, with his seventh-minute penalty putting Italy on the right track at Ta' Qali.
Gianluigi Buffon did have to deny Malta's Michael Mifsud from the spot, though, before Balotelli found his second goal at the end of a devastating team move just before the break.
Italy did enough against a lacklustre Malta side to pull three points clear of Bulgaria, who reached 10 points with a 1-1 draw in Denmark.
Malta remained bottom of the group without a point.
Cesare Prandelli's team selection was unusual in the fact he picked six Juventus players and five from Serie A rivals Milan to start tonight's game.
Of that group, one man has stood out in Italy and across Europe over recent months.
And Balotelli did not need long to make his mark in Malta as referee Serdar Gozubuyuk pointed to the spot inside seven minutes.
Luke Dimech tripped Stephan El Shaarawy in the box moments before Balotelli stepped up to send Justin Haber the wrong way.
El Shaarawy fancied a goal of his own but his curling effort whistled wide before Malta were thrown a lifeline in the 16th minute.
When Andre Schembri caught Claudio Marchisio cold in midfield, all Buffon could do was smother at the Maltese's feet and bring the player down. The Juventus keeper made amends, though, guessing right to parry Mifsud's penalty.
It was a frustrating moment for Mifsud and he would have another moments later as his dipping drive found the crossbar.
Italy turned the screw for the rest of the half and, despite Jonathan Caruana missing from six yards, it was a one-sided run to the interval.
Balotelli dummied El Shaarawy's pass into Riccardo Montolivo, but the ball ended up on the roof of the net before the former whipped a dangerous strike just wide of the target.
Italy and Balotelli grew frustrated as an Andrea Pirlo free-kick hit the wall and Montolivo fired over the bar from close range, but the travelling supporters received a timely boost just before the break.
In a fluid team move orchestrated by Mattia De Sciglio the Milan defender swept up Leonardo Bonucci's pass to beat his man to the by-line, where he pulled the ball across the six-yard box for Balotelli to steer it home with the side of his boot.
Malta needed a smart save from Haber from Emanuele Giaccherini to keep the scoreline to two when play resumed, with Andrea Barzagli heading wide from the resulting corner.
The Juve defender then denied Mifsud who came sniffing from 12 yards on the counter-attack.
El Shaarawy had hearts in mouths when he shot flush into Haber's gloves from six yards out but the second half did not live up to the excitement of the first.
Bologna's Alberto Gilardino, another Milan alumnus and Balotelli's replacement tonight, went dangerously close with a header as time ticked away but the damage had already been done by the Rossoneri's latest Italian star.