Police stepped in to protect the referee from furious Udinese protests after yet another in a series of hugely controversial decisions which have marked Serie A this season.
Italy striker Balotelli, who had opened his account in the 25th minute three days after completing his big-money move from Manchester City, converted with the last kick of the match after the referee judged that Stephan El Shaarawy had been fouled.
El Shaarawy tumbled theatrically in the area after being tackled by Thomas Heurtaux but the referee pointed to the spot amid Udinese disbelief and "Supermario" converted.
Giampiero Pinzi had levelled for Udinese early in the second half after Balotelli opened his account when he turned in El Shaarawy's cross from six yards.
Leaders Juventus, themselves involved in a furious row one week ago over the refereeing in their 1-1 home draw with Genoa, won 2-1 win at Chievo, restoring their three-point lead at the top. Lazio and Inter Milan lost touch after losing to lowly opponents.
Alessandro Matri volleyed home after 10 minutes and Switzerland midfielder Stephan Lichtsteiner finished a well-worked move three minutes before half time for Juventus, whose new signing Nicolas Anelka was left on the bench.
Cyril Thereau pulled one back for the Flying Donkeys early in the second half but Juventus, with coach Antonio Conte barred from the touchline for his furious outburst over the refereeing against Genoa, held out comfortably.
Genoa's Marco Rigoni headed in from a corner in the fifth minute of stoppage-time to give them a 3-2 win over third-placed Lazio, who slumped to their second successive league defeat despite coming back from two goals behind.
Marco Borriello and Andrea Bertolacci struck in a six-minute spell in the first half to put Genoa in control before Sergio Floccari pulled one back and Stefano Mauri levelled with an 82nd-minute penalty.
Inter produced a dire performance in a 3-1 loss at table-propping Siena which left coach Andrea Stramaccioni fuming and meant they dropped to fifth, behind rivals AC Milan.
"It was an ugly defeat and an ugly performance and there is no justification for it," he told RAI television.
"We've got to find ourselves again, as we are still the team who in November were a point off the leaders and had great ambition."
There were three goals in a four-minute first-half spell as Siena's debutant Innocent Emeghara tapped in from close range, Antonio Cassano levelled almost immediately and Alessio Sestu put the hosts back in front with a long-range effort.
Siena wrapped things up 10 minutes after the restart after Inter's Cristian Chivu hauled down Emeghara, was sent off and Alessandro Rossina converted the penalty.
Juve have 52 points from 23 games, Napoli 49, Lazio 43 and Milan and Inter 40.
Siena's win took them off the bottom of the table on goal difference from Palermo who lost 2-1 at home to Atalanta, despite fielding four new signings.
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