The pair exchanged insults in the final minutes of Friday's 4-1 win over Palermo, it was reported he will be left in the stands.
“Tomorrow Bonucci will be in the stands. That doesn't mean it has to be made into a big deal. Out of respect for the club, the team and the fans, this was the right decision.
“The case is closed. Leo understood the situation, as an intelligent lad and important player for Juventus. It's a moment that will be useful for the future.
“I also had a reaction that was not right and not suited to the way I see football, above all with fans and children watching, so tomorrow I will give a charity donation."
Allegri was asked why Bonucci was punished, but not Paulo Dybala or Stephan Lichtsteiner for their irritated reactions to leaving the field this season?
“Things happened and that's it. If Bonucci was the first to react like that, he might not have paid such a heavy price. It's the rule of life – someone has to pay.
“I will give you four starting players: Cuadrado, Higuain, Dybala and Mandzukic. Will Miralem Pjanic play? You are asking that so you know if it's the five stars, aren't you? Clever. Well, Pjanic will play.
"Barzagli and Chiellini are fine. It's an important moment of the season, four will go in the stands, but we have Empoli and Napoli coming up, so it's crucial all the players stay together as a group during this period.
“There are tensions and a bit of chaos during a season, that's part of the sport, but we don't need to make things worse than they are. It is all sorted out, we move forward.
“We have to keep the focus on the most important thing, which is the game. These are 180 very difficult minutes, Porto are the worst side we could've drawn in the Round of 16 and we do not want to be distracted by a situation that does not exist.
“Nothing else happened. I spoke to Leo, he understood and we move forward."