Ivanovic, who faces a three-match ban if found guilty, was caught on video appearing to strike Latics midfielder Maloney in the midriff moments before Juan Mata's controversial winner in the Blues' 2-1 Barclays Premier League victory at Stamford Bridge.
Referee Mike Jones confirmed he and his assistants did not witness the incident, giving the Football Association the green light to investigate it retrospectively.
Ivanovic, 28, was given until 6pm on Wednesday to respond to the charge.
The video footage, which emerged after Saturday's game, shows Maloney going down bent double following the clash.
Ivanovic faces being banned for Chelsea's FA Cup semi-final against Tottenham on Sunday and two further derbies against Arsenal and QPR in the league.
The defender has been one of the Blues' best players this season, once again making the problem right-back position his own, and his absence would be a huge blow to the club's hopes of finishing in the top four.
With left-back Ashley Cole also struggling with an ankle injury and captain John Terry playing through the pain of two broken ribs, caretaker manager Roberto Di Matteo could be left with a real defensive headache.
Any punishment for Ivanovic would only add insult to injury for Wigan boss Roberto Martinez after the officials failed to chalk off both Chelsea goals for offside on Saturday.
The Spaniard insisted on Tuesday he did not want to see Ivanovic banned, possibly because he would miss a game against one of the Latics' relegation rivals.
"As a player, if you do something wrong you should be punished at that moment," Martinez said.
"You are competing against the opposing team in that game. You should be punished there and then.
"I don't see the point of punishing someone retrospectively. That is not something I am keen to see."