Two trademark headers from the 36-year-old former Italian international in the 29th and 53rd minutes gave promoted Verona a deserved three points in the opening league game of the season.
Milan produced a disappointing display despite taking a 14th minute lead through Andrea Poli who was also making his debut for the away team.
The win brought delight to the fans at the Stadio Bentigodi who have had to suffer for more than a decade in the second and third tiers of Italian soccer while their smaller local rivals Chievo Verona flourished in Serie A.
After the mayor of Verona said on Friday that Mario Balotelli brought abuse on himself, the home side's notorious supporters chose to ironically applaud the Milan striker and chant his name instead.
"We talk too much about this, I think the people gave their response today," Hellas Verona midfielder Massimo Donati told Sky Sports.
"I hope this is the start of a season full of celebrations and disappointments but conducted in a civil fashion."
As Donati spoke, however, the away fans ripped up seats and launched them at their Verona counterparts after the game.
Poli put Milan ahead when he took a smart pass from an otherwise subdued Balotelli before weaving his way past two defenders and providing a calm finish.
Massimiliano Allegri's side had the hosts on the back foot at that point but Verona, among the favourites to be relegated, seized control of the midfield with some hard pressing and levelled the score through Toni.
Verona started the second half much the brighter and could have had the lead six minutes after the break when Christian Abbiati did well to tip over a powerful Bosko Jankovic header.
Two minutes later the Serb clipped in a perfect cross with the outside of his right foot for Toni to score his 110th Serie A goal with another well-placed header.
Milan poured forward in desperation and it was only poor passing in the final third of the pitch that let Verona down as they capitalised with numerous counter-attacks.
"They deserved to win. We started well and then we stopped playing. We need to play with more aggression," said Allegri.
"We have to have a different attitude. We had it for 14 minutes and then we started to make mistakes and expose ourselves to counter-attacks."
Champions Juventus begin their bid for a third successive title with a trip to Sampdoria in Saturday's late game.
(Reporting by Terry Daley; editing by Tony Jimenez)
