Mancini found himself at the centre of controversy once again after waving an imaginary card in the 88th minute of City's 1-0 win at Wigan on Monday after Maynor Figueroa had handled to deny Sergio Aguero a run at goal.
It is the second time Mancini has been pictured trying to influence the referee from the sidelines in two weeks.
The Italian issued a public apology after admitting he made "a mistake" by campaigning for Martin Skrtel to be dismissed when the Liverpool defender gave away the penalty from which James Milner scored City's third goal during the 3-0 league defeat of Liverpool on January 3.
And Mancini was also involved in a post-match row with Steven Gerrard for suggesting Glen Johnson deserved a red card for a two-footed challenge on Joleon Lescott during Liverpool's League Cup victory at City last week.
Rooney was forced to defend himself after Mancini accused him of putting pressure on the referee to get Vincent Kompany sent off in City's 3-2 FA Cup defeat by United on January 8.
And Rooney took to Twitter to have a go at Mancini's actions towards the end of City's narrow victory over Wigan.
"Was manchini (sic) asking for a red card????" Rooney wrote on his official Twitter account.
Mancini defended his actions and insisted: "I used to do this (card waving) but I don't want to say anything. I did it because Wayne Rooney did this but it's normal with a chance like that.
"I am on the bench. When you are near to the referee you can have more of an influence.
"I am on the bench and the referee cannot see me."
City moved three points clear at the top of the table after Edin Dzeko's goal saw the Premier League leaders return to winning ways after back-to-back cup defeats.
Defender Micah Richards and striker Mario Balotelli missed the Wigan match with hamstring and ankle injuries respectively and Mancini refused to be drawn on whether they will make Sunday's home game with third-placed Tottenham Hotspur.
"I hope they will both be back on Sunday, but it is difficult to say. Micah has a hamstring injury but it is not serious," he added.
Dzeko's effort ended a two-month goal drought.
"We could have scored one or two more but at the end we are happy with the three points because we didn't play that well," said the 25-year-old Bosnian.
"I am happy to score again."
Meanwhile, Wigan manager Roberto Martinez insisted Figueroa's handball was not a sending off offence.
"I don't think it's a goalscoring opportunity," said the Spaniard.
"I've been here long enough to understand that trying to influence the referee is not accepted in the British game.
"When a player tries to simulate or buy a decision from the referee that is regarded as cheating.
"I understand that in Italy, France and Spain it is acceptable to try and get a decision from the referee, but it is different here."
Wigan - who only avoided relegation on the last day of last season - remain bottom of the Premier League two points adrift of safety.