The Italy forward won the penalty after being pulled down by Davide Astori and sent Michael Agazzi the wrong way to make it three goals in two games for fifth-placed Milan since his move from Manchester City.
Astori, already booked for a previous foul on Balotelli, was sent off as Cagliari faded in the second half after dominating the opening 45 minutes and taking the lead with a Victor Ibarbo header.
Milan coach Massimiliano Allegri described his team's result as "a useful point against a good team."
"Today, we had four players on the pitch who were born in 1992," he added.
Palermo and AS Roma, who fired their coaches after losing their previous games, failed to win, but Inter Milan beat Chievo 3-1 to ease the pressure on coach Andrea Stramaccioni.
Pablo Osvaldo missed a penalty for Roma in their 3-1 defeat at Sampdoria as they remained winless in the league in 2013.
Juventus, who beat Fiorentina 2-0 on Saturday, are top with 55 points, five clear of Napoli who drew 1-1 at third-placed Lazio, also on Saturday.
Lazio are a further six points behind in third and only one ahead of Inter.
Palermo stayed level on points at the bottom with Siena after drawing 1-1 with Pescara, who are also in the relegation zone.
Alberto Malesani, taking over as Palermo's third coach of the season following the dismissal of Gian Piero Gasperini, saw his side fall behind to a 73rd-minute header by Birkir Bjarnason.
Diego Fabbrini, signed on loan from Udinese in January, levelled in the 80th minute for the Sicilians who have 18 points from 24 games, three behind Pescara who are 18th in the 20-team table.
Paraguay midfielder Marcelo Estigarribia gave Sampdoria the lead against Roma in the 55th minute as Aurelio Andreazzoli moved into the hot seat on an interim basis following the dismissal of Zdenek Zeman.
Osvaldo then won a penalty for Roma, insisted on taking it despite protests from the usual taker Francesco Totti and weakly sent it into the arms of Sergio Romero.
That was followed by three goals in five minutes as Gianluca Sansone curled in a free kick for Sampdoria, Erik Lamela volleyed one back and 19-year-old Argentine Mauro Icardi restored the two-goal lead with a header.
Diego Milito scored his first goal of the year early in the second half to complete Inter's win over Chievo.
Antonio Cassano, overlooked by Italy since Euro 2012, gave Inter a second-minute lead, helped by a blunder from Chievo goalkeeper Cristian Puggioni.
Luca Rigoni levelled in the 21st minute after being left unmarked to head in but Inter, who had won only one of their last seven league games, quickly re-gained the lead when Andrea Ranocchia headed in from a corner.
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