The points were shared in Prague as a lacklustre Italy side rarely threatened Petr Cech in the hosts' goal, while visiting goalkeeper Gianluigi Buffon was forced to repel dangerous attempts from Libor Kozak and Petr Jiranek.
As time ticked away the Azzurri seemed content to settle for the point that built a four-point cushion over Bulgaria at the top of Group B but Balotelli's dismissal for two yellow cards in three minutes made for a tense finale in the Generali Arena.
Prandelli told figc.it: "Mario was very nervous. He conceded a lot of fouls and fell into the trap of reacting to provocation. He has to learn how to deal with certain situations and improve from that point of view.
"We're trying to make him understand. I was planning to substitute him but I ran out of time."
Even if the performance was sorely lacking, Italy can now fly to Brazil for next week's Confederations Cup secure in the knowledge their World Cup destiny is in their own hands.
"It is a very valuable point," Prandelli added. "We were not in sparkling form, though, we were slow in our movement and were too slow on the counter-attack.
"We went into the game at the end of a tiring season and found it difficult without a full tank. But these games are character building and we wanted the point, which we deserved, at all costs.
"In terms of character we never gave up and that's the important thing."
Juventus keeper Buffon could state a strong case for having earned Italy the draw single-handedly as he closed down Kozak in a surprise one-on-one before tipping the Czech's fierce shot over the bar and pushing Jiranek's late effort onto a post.
The 35-year-old said: "It's an important point that allows us to go into the last run of games with a big advantage and three of the remaining games are at home.
"When you haven't played for a month it can be difficult to get into these kind of games.
"Balotelli's dismissal? He was really sorry in the changing rooms, he'd picked up a double booking that could have happened to anyone.
"These things happen on the pitch but I didn't see him do anything particularly serious.
"It would be worse to see a player who wasn't fighting for the shirt, but we've never had that kind of problem here."