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.
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.
"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.
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.
