The Italy striker had scored 12 goals since arriving at San Siro in January but failed to fire in a shock 2-1 defeat at Hellas Verona on the opening weekend of the 2013-14 campaign.
He improved on home turf to engineer goals from Robinho and Philippe Mexes and, after Marco Sau had responded emphatically for the Sardinians, Balotelli made sure to rubber-stamp the three points.
Milan's qualification for the Champions League group stage had generated some good feeling but the Rossoneri needed a spark to ignite their domestic season.
It arrived inside eight minutes but not through a familiar source as Robinho scored his first Serie A goal of the calendar year.
The Brazilian, who came close to joining Santos last month, swept up a Balotelli cross from the right to tuck the ball home from nine yards.
With Cagliari on the ropes Robinho came close to adding a second but his radar malfunctioned as he shaped to shoot at the end of a mazy dribble.
The game settled into a steady rhythm, briefly, until Balotelli sparked a frenetic exchange of goals on the half-hour mark.
It was Balotelli who created space and time to test Michael Agazzi with a low shot but it fell to Mexes to volley the ball home with a dramatic scissor kick from six yards out.
Cagliari's response was as surprising as it was clinical as Sau brushed off a clutch of Milan defenders to skip on to the D before rifling the ball into the top corner.
The goal hushed the San Siro crowd and they would not cheer again until Balotelli shaved paint off a post with a fearsome free-kick from distance shortly before the break.
Radja Nainggolan came closest to equalising following the restart as he seized on Mauricio Pinilla's sweeping cross, but Ignazio Abate stepped forward to force a corner.
The islanders would be punished for not making more of the move as Balotelli widened the gap just after the hour.
Abate was on attacking duties when his short cross arrived at Balotelli's feet - the Italy striker slamming home under the bar before pumping his fist in celebration.
As time ticked away former Cagliari striker Alessandro Matri was given a brief run-out from the bench following his signing from Juventus.
Sau might have inspired a frantic finale by completing his brace in the late exchanges, but he failed to capitalise on an error from Cristian Zapata and instead clipped the ball into Christian Abbiati's gloves.