The Italy striker is Milan's top scorer this season with three goals but must complete his three-match ban this weekend.
Balotelli was able to play in midweek, earning and scoring a penalty to hand Milan a 1-1 draw at Ajax Amsterdam in the Champions League.
"It's a pity that Balotelli will not be available for Juve," Allegri said. "It will weigh heavy on the team because he has important qualities but I'm confident my team will do well."
Balotelli watched from the stands last Sunday as Milan beat Sampdoria 1-0 to end a three-match winless run.
The result was Milan's second league victory of the campaign and lifted the Rossoneri to ninth place.
With Balotelli out, Allegri is hoping Alessandro Matri can end his goalscoring drought.
Matri, who won two league titles with Juventus, has failed to find the back of the net in seven appearances for Milan.
Juventus defender Giorgio Chiellini thinks the Rossoneri are more than capable of putting in a good performance.
"Without Balotelli, all the other players will give a lot more," he said. "In any case Milan will have Matri, a great player that we know well.
"We wish him well but hope that he will not score on Sunday."
Juve are unbeaten and hold an eight-point advantage over Milan after six games.
Last weekend's 1-0 triumph at Torino marked their third straight league victory and lifted the Bianconeri to third place, two points behind Serie A leaders Roma.
The Italian champions head into the contest frustrated by their midweek 2-2 home result against Galatasaray in the Champions League.
Antonio Conte's men went close to earning their first win in Group B only to be denied by Umut Bulut's 88th-minute equaliser.
Juventus will be without midfielder Stephan Lichtsteiner and striker Mirko Vucinic.
Both players sustained muscle injuries in midweek and will not recover in time for the game.