The Azzurri conceded twice in each half as they were overpowered by the defending champions.
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."
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Strangely, Italy enjoyed the majority of possession in the first-half but still found themselves two goals down through David Silva and Jordi Alba.
However, an injury to their final substitute, Thiago Motta, within four minutes of his introduction, forced Italy to complete the final half hour with 10 men.
And, in their 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.
The Italy manager confirmed both Motta and Giorgio Chiellini, who had to be replaced in the first-half, had both suffered hamstring injuries.
European Championship Winners
1960 - USSR
1964 - Spain
1968 - Italy
1972 - West Germany
1976 - Czechoslovakia
1980 - West Germany
1984 - France
1988 - Holland
1992 - Denmark
1996 - Germany
2000 - France
2004 - Greece
2008 - Spain
2012 - Spain