He stated that he was "hurt" by the Manchester City striker's decision to schedule laser eye surgery during the last international break.
Balotelli was among six players recalled by Prandelli for the qualifying double-header after missing games against Malta and Bulgaria last month as he recovered from the procedure.
Prandelli felt it was unfortunate that Balotelli put his club commitments before those of his country, but admitted that - given the striker's stunning form for the Azzurri at Euro 2012 - it would have been wrong to leave him out of his selection on this occasion.
"I tell you the truth, when he decided to undergo surgery just two weeks before his commitments to the national team, there was hurt," Prandelli told a press conference.
"We now need to understand if he wants to become a champion. The blue shirt is a wonderful thing for all players.
"I had some thoughts (about dropping him), but then I thought of the games he has played for his country and I was comforted."
Domenico Criscito, Alberto Gilardino, Andrea Ranocchia, Antonio Candreva and Stephan El Shaarawy were also welcomed back into the fold when Prandelli named his 27-man squad on Sunday, but there was no place for either Inter Milan striker Antonio Cassano or Udinese hitman Antonio Di Natale.
"Why have not I called Antonio? I don't consider his or Antonio Di Natale's cycles to be over," Prandelli said.
"Right now, I want to try out a few younger players. But they will be up for consideration again if they are in the right condition."
Zenit St Petersburg defender Criscito was recalled after being sent home from the European Championships due to a betting investigation.
The 25-year-old former Juventus man was never charged and Prandelli added: "I am delighted to have Criscito available again. Now that everything has been resolved I can again consider him.
"The decision to leave him out of Euro 2012 was very painful on a technical and human level.
"I'm sure that he'll forget all about it once he steps out on to the pitch."
Italy travel to Armenia for their third Group B qualifier this Friday, before facing Denmark at the San Siro in Milan next Tuesday.
Prandelli's men are bidding to rediscover the form that took them all the way to the final of Euro 2012 after opening their World Cup qualification bid with a 2-2 draw in Bulgaria and an underwhelming 2-0 home win against Malta.
"These are two delicate games - important and perhaps decisive," Prandelli said.
"I am convinced that the mistakes made in the first qualifying matches will not be repeated again."