The focus was supposed to be on Kaka, who was making his long-awaited second debut for Milan after spending four years at Real Madrid, but Torino stole his thunder with a double salvo in the second half.
Captain Danilo D'Ambrosio and Alessio Cerci set Il Toro on course for a first win over Milan since November 2001 and Sulley Muntari's sloppy response seemed to have arrived much too late.
Balotelli had cut an anonymous figure through 90 minutes in Turin but made the headlines by converting a penalty - won by Andrea Poli - four minutes into stoppage time.
While travelling Milan fans lapped up Kaka's every touch in the opening exchanges, Torino made themselves busy dominating the first half at the Stadio Olimpico.
Cerci's ball through for Ciro Immobile skipped beyond the poorest of challenges from Cristian Zapata and the visitors were only spared by the quick thinking of goalkeeper Christian Abbiati.
In the ninth minute Giuseppe Vives launched an audacious sighter from 30 metres but the ball swerved wide of Abbiati's goal, before Milan captain Riccardo Montolivo tried to catch Daniele Padelli napping at the other end.
The Torino keeper was wise to the move and, after Philippe Mexes' heavy pass went out of play rather than on to Kaka's feet, the hosts came knocking once again.
Zapata managed to close Vives down in a shooting position but no one was covering Immobile as he rifled a searing strike slightly wide of the mark.
Milan playmaker Montolivo was struggling and was replaced by Poli in the minutes leading up to half-time, but not before handing the captain's armband to Kaka.
The Brazilian clearly did not have enough time as team leader to steel his colleagues against a likely Torino raid following the restart, and it would come.
In the 47th minute, full-back D'Ambrosio found himself in the unnatural position of cutting in from the left wing, where he showed a striker's composure to dummy Cristian Zaccardo and slot home at the near post.
Milan, who now knew they had to produce something if they were to avoid a second defeat in three games, seemed out of ideas and Balotelli's scooped shot from close range was certainly not the required response.
Kaka soon began to tire and, after he was withdrawn for Valter Birsa, Milan's night took another turn for the worse.
There were 71 minutes on the clock when Cerci seized on an error by Balotelli to sprint from the halfway line and chip the ball over the kneeling Abbiati.
It had seemed a rare off night for Balotelli and his failure to beat Padelli in an easy one-on-one was symptomatic of Milan's general malaise.
The Rossoneri would, however, halve the deficit in scruffy fashion as time ticked away.
Muntari twice made a mess of shots from the D, but the Toro backline failed to clear on both occasions and they were punished as his third attempt bobbled into the far corner while Padelli kept one eye on Balotelli.
And while Torino boss Giampiero Ventura was preparing to make a late substitution to wind down the clock, Poli was tumbling over Manuel Pasqual's legs on the right side of the penalty area.
A lengthy delay as protests filled the air could not delay the inevitable and Balotelli steered his spot-kick beyond Padelli with the minimum of fuss.