The 21-year-old Italian was sent off for two bookable offences only 18 minutes after coming on as substitute.
"I do not agree with this [second] yellow," said Mancini. "The referee didn't want to get a yellow card out.
"I think the referee gave a free-kick but didn't want to give a yellow until all the Liverpool players complained."
Media playback is not supported on this device
Balotelli's first yellow card at Anfield, for pulling back Glen Johnson, was not disputed by his manager - but Mancini was adamant the second, for catching Martin Skrtel with an arm, was unjustified.
It was the third time Balotelli has been dismissed in his eventful City career, during which he has thrown a dart at a youth team player, been substituted after an allergy to the pitch in Kiev and escaped after a firework was let off in his bathroom.
Mancini added: "I watched the replay and, for me, it is nothing. This situation in the Premier League - there are a lot [of yellow cards] in every game. I don't think all [the fouls] are yellow cards. Mario should pay attention because he knows many players provoke him and this is not correct."
There were also reports that the forward damaged a door in the City dressing room after he had to be told by Mancini to head down the tunnel following his dismissal.
November 2010 at West Brom
March 2011 v Dynamo Kiev
"I don't know this. If he damaged the door he pays - like his house," said the City boss, in reference to Balotelli's firework incident last month.
Liverpool manager Kenny Dalglish had no sympathy for the Italian, however. He said: "I think Balotelli got himself sent off. His actions spoke louder than anybody else's didn't they? Sometimes, if you look in the mirror, you get the answer.
"Sometimes he doesn't help himself, other times he doesn't get as much leeway as anyone else gets.
"But, if you help yourself, you don't get in that situation in the first place."
Manchester City boss Roberto Mancini says Liverpool's players were to blame for the dismissal of Mario Balotelli in the teams' 1-1 draw at Anfield.