Mancini began gesticulating from the sideline after Maynor Figueroa deliberately handled the ball late in the game at the DW Stadium, stopping Sergio Aguero running through on goal. The incident comes just a few weeks after the Italian wanted Martin Skrtel sent off during City's 3-0 victory over Liverpool.
On that occasion Mancini apologised for his actions, but he then criticised Rooney for waving an imaginary card to get Vincent Kompany dismissed in the FA Cup third round tie between City and Manchester United.
When Mancini produced a similar gesture on Monday after Figueroa's indiscretion, Rooney tweeted: "Was Mancini asking for a red card???"
On this occasion the City boss rejected the suggestion that he had acted out of turn, insisting there is a gulf in difference between the influence a player can have on a referee compared to the sway held by a manager.
"I did it because Wayne Rooney did it," Mancini was quoted as saying in The Sun. "It is normal with a chance like that to do it.
"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."
However, when Mancini was asked if he was wrong to criticise Rooney for his gesture at the Etihad Stadium, Mancini replied: "Yes."
City won Monday's encounter 1-0 thanks to an Edin Dzeko header, but Mancini's touchline antics were borne out of some nervy moments in the closing stages. Nevertheless, Wigan boss Roberto Martinez told the Italian he has to learn to curb his emotions.
"I have been here long enough to know that trying to influence the referee is not acceptable in Britain," Martinez said. "I understand that in France, Italy and Spain it is accepted but it is different here."
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