The temperamental 21-year-old scored his first European Championship goal against Republic of Ireland on Monday, but celebrated with what appeared an angry tirade before team-mate Leonardo Bonucci shut him up with a fatherly hand over his mouth.
Balotelli was left on the bench by Prandelli for Italy's third and final Group C match, having started the previous two.
It wasn't clear who his ire after scoring was aimed at, but Bonucci claimed he hadn't understood as Balotelli was talking in English and Prandelli said he too didn't know. But he hit out at the Manchester City striker, saying he needs to learn to take the rough with the smooth and to never forget that there is no 'I' in team.
"Right now the spirit of the team is important, what matters on this journey is that every player called up gives 100 per cent," said Prandelli. "That's what I like because it means they have great respect for the team and when that's the case they also run for the team.
"[Balotelli] came on and did what we asked of him, which was to play between the two (Irish) centre-backs and interrupt their co-operation. Also to put some weight into our attack and he did well, he knew his role and what to do."
Prandelli said this on Balotelli's reaction after scoring: "As for smiling, his reaction was spontaneous. As for his behaviour he's always like this, therefore it wasn't strange. He's not an outsider in the squad, Mario's like this, it depends on the moment and his mood.
"In uncomfortable moments you have to accept this peculiarity. He needs to take a step up in quality but he can do that. He must accept difficulties and criticisms and also to be on the bench or that the team ask for more from him.
"The day that he realises that no-one wishes him any harm and that all they want is to help him develop, then he'll become a great player."
As for Bonucci's damage-limitation exercise, Prandelli said that showed how popular Balotelli is within the camp. "You could also see the spirit of the team in this gesture, which was a protective one. It was worth it because certain things inside should be managed personally, I was very happy with Bonucci."
Although he criticised Balotelli's attitude, Prandelli seemed understanding of the difficulty a player such as the 21-year-old has in coping with tough situations. However, he said Balotelli had shown against Republic of Ireland that he can be a team player.
"Often these type of players with this sort of temperament and pride bring it out in difficult moments because they want to show you what they can do," he said.
"But we were clear with Mario, this wasn't an opportunity for you, it was an opportunity for us as a team and you can still make a difference even in these 20 minutes. For me, Mario's 20 minutes was the best he played in the three games."