Kagawa broke a bone in his foot during Tuesday's semi-final victory over Korea Republic, an injury that might sideline the Borussia Dortmund midfielder for the rest of the season.
The 21-year-old had proved instrumental in Japan's march to the final, his two goals against Qatar in the last eight helped the Samurai Blue come from a goal down with 10 men to knock out the hosts, and Zaccheroni admitted Kagawa is a big loss.
“It's very disappointing for the team and him as well,” said the Italian.
“He contributed a lot to the team on the way to the final and he was getting better and better so it's very disappointing. I know who's going to replace him, I know him well and I trust him.”
Japan take on Australia at Khalifa Stadium in a clash of the competition's two most prolific teams and Zaccheroni has been pleased with the way his youthful squad have overcome every challenge they have faced.
“I am very satisfied to make the final and I like the way we got here. I give the credit to our players because we had many difficult matches,” he added.
“Game by game we've been organised, especially against the Middle East teams. We've had some difficulty against them in the past.
“There are many qualities to our football, so it's difficult to pick one but maybe it’s the togetherness of this team. The spirit of this team is fantastic. It makes me proud to be in charge of this team.
“Since I've been in charge, people have told me we dislike playing against Middle Eastern teams and Korea. Throughout this competition, I haven't felt that at all. I tell the players to respect other teams but not be scared of them. I think the players understand that and they will have that attitude.
“I like to look at the balance the most. If you have players motivated too strongly that's not always a good direction so I'd like to keep them calm.”
Regardless of the outcome on Saturday, Zaccheroni feels Japan's performances in Doha indicate they are set to become a force on the international stage for years to come.
“I cannot really tell you the percentage this team has improved by but the potential of this team and the players is immeasurable,” he said.
“I wanted this team to get more experience here, especially to improve the young players through this competition.
“The goal is to make a good team for the World Cup. This team's base is the playing style of the J.League and I would like to add something to it and play positive football. Through the difficult matches in this competition, we have improved not only the physical, tactical and technical aspects but also our mental ability a lot.”