The Italian veteran helped conjure up a surprise opening day defeat for the Rossoneri after Andrea Poli had given them the lead
Andrea Poli seemed to have the visitors on course for three points when he struck after quarter of an hour but Toni replied either side of half-time to give the underdogs an unexpected victory.
Andrea Mandorlini made three changes from the side that defeated Palermo in the Coppa Italia last weekend.
Romulo, Bosko Jankovic and Fabrizio Cacciatore all came in at the expense of Alessandro Agostini, Daniele Cacia and Jacopo Sala.
Massimiliano Allegri named four changes from the side that drew 1-1 with PSV Eindhoven in midweek.
Kevin Constant, Antonio Nocerino, M'Baye Niang and Poli all came in to the side in place of Kevin Prince-Boateng, Nigel De Jong, Urby Emanuelson and Sulley Muntari.
Riccardo Montolivo had the first effort of the game, firing just over from outside the box in the second minute.
Mario Balotelli then went close as he saw his shot well saved by Rafael low to his right.
Poli opened the scoring after 14 minutes, running on to Balotelli's pass before slotting past Rafael.
Balotelli continued to threaten for the visitors, as the striker saw a well-struck free-kick dip just too late to trouble the goalkeeper.
Verona's first effort on target came midway through the half as Raphael Martinho's volley from distance was comfortably held by Christian Abbiati.
But despite having failed to significantly test their visitors, the hosts drew level with 30 minutes on the clock.
Toni met a corner from the right with a thumping header beyond Abbiati from six yards.
The striker went close to giving his side the lead five minutes later, but this time the goalkeeper was down smartly to his right to parry the shot.
Toni was again on target as the half drew to a close, rising to meet Jankovic's cross, but his header lacked the power to seriously trouble Abbiati.
Jankovic went close to giving Verona the lead early in the second half, but his firm header from Martinho's free-kick was tipped over the bar.
They did not have to wait long, however, as a minute later Toni nodded them in front from Jankovic's perfectly weighted cross using the outside of his right boot.
Balotelli then had a close-range effort blocked after Philippe Mexes had made a mess of an attempted overhead kick when it looked simpler to head the ball towards goal.
As Milan pressed, Verona broke swiftly and Abbiati had to fly to his left to cut out Martinho's cross-shot in the 65th minute.
With the game entering its final stages, Balotelli tested Rafael with a curling effort from distance and Domenico Maietta was forced to clear over his own crossbar, but Milan could create no further chances as Verona held on for the win.