The Azzurri conceded twice in each half as it was overpowered by the defending champion.
It left Balotelli shattered after he had gone into the game with such high hopes.
The Manchester City man stormed straight down the tunnel at the final whistle, and angrily shrugged off the attempts of Italian officials to stop him.
Balotelli eventually returned to collect his medal.
"I told Mario that these are experiences you have to deal with and have to accept," said Prandelli.
"You have to hold your hands up and say the opponents were better, accept defeat.
"But you also have to make sure this helps you going forward and you can grow from the experience.
"This has happened to a number of players, and will happen again, but this is what sport is all about."
However, an injury to its final substitute,
And, in its third game in a week, which included that draining period of extra-time against England, it was too much.
"We've had a terrific European championship and the only regret is the fact we didn't have a few extra days to rest up before this game," said Prandelli.
Azzurri captain Gianluigi Buffon was magnanimous in defeat.
He told BBC Sport: "Tonight, there was no contest, they were too superior - so the bitterness at losing this final is only relative.
"It was a great adventure. In a final, you have to win but today we played against a team of incredible quality."
UEFA president Michel Platini said preparations for Euro 2016 were "progressing well" after a meeting of the organising committee in Lille.