The striker broke down in tears shortly after being substituted as he watched his side slump to a 3-1 loss at the San Paolo on Saturday, with initial rumour on social media incorrectly suggesting racial abuse from home supporters had prompted his reaction.
Prandelli feels Balotelli was simply overwhelmed following a turbulent week in which he learned he was the biological father of Pia, the daughter of ex-girlfriend Rafaella Fico, and believes the 23-year-old's reaction sends a positive message about the pressures involved in the game.
"He has recently acknowledged his daughter, but I'm not going to get into his personal life as a matter of respect," Prandelli told Tuttosport. "But thank goodness that he burst into tears the other night on the bench.
"I think he was overwhelmed by strong emotions at Napoli. He's young and cannot always handle extraordinary pressure.
"His tears were not a sign of weakness, they showed he is human. They represent a good message - superheroes do not exist. He showed he understands the fragility of being a human like everyone else.
"We should never be ashamed of our feelings."
Prandelli went on to discuss Pablo Daniel Osvaldo's move to Juventus in January, claiming the on-loan Southampton forward will mature under Antonio Conte.
"Osvaldo's been waiting for a breakthrough," Prandelli said. "His arrival at Juventus will increase the motivation of the group, while Juve is an extraordinary opportunity for him to mature and grow.
"This experience has come at the right time for him."
Finally, Prandelli stated his Italy side should not be considered favourites for the World Cup this summer, but admitted certain Azzurri veterans could serve as inspirational figures for future generations.
"The favourites are Brazil, Argentina, Spain and Germany. Then there is us, Uruguay, England, Holland, Belgium, Colombia, Japan," added the 56-year-old.
"I am lucky to have players like [Gianluigi] Buffon, [Daniele] De Rossi and [Andrea] Pirlo. They always concentrate. They are also world champions that can show their motivation to future generations."