In an uncanny repeat of the 2013 FA Cup final, in which City had a player sent off before losing to a late Wigan victor, Guardiola's side had Fabian Delph dismissed amid stormy scenes before Will Grigg's 79th-minute goal decided the game.
Both clubs have until 6pm on Friday, February 23, to respond to the charges.
Yet it is also thought players and staff from both sides have avoided punishment from the FA for the half-time row involving City boss Pep Guardiola and his Wigan counterpart Paul Cook.
Will Grigg scored the only goal of the game after 79 minutes to book a quarter-final tie against Southampton for Paul Cook's League One promotion-chasers and end the runaway Premier League leaders' prospects of a historic quadruple.
Sergio Aguero has claimed that he hit out at a Wigan supporter in the aftermath of Man City's FA Cup defeat to Wigan at the DW stadium because he was spat at.
The incident saw Aguero being restrained by other members of the squad as he looked infuriated and determined to lock horns with a random fan who had confronted him.
City will now speak to Wigan in the coming days to demand an explanation of why supporters were allowed onto the pitch.
During a tightly-contested second-half, when City's expectantly controlled most of the ball, Wigan'sWill Grigg got the all important goal for the hosts and set in action a stunning scene for Wigan's joyous supporters.
The FA has now charged both clubs with failing to control their players and staff, but there will be no individual action against Guardiola.
"There's no problems", said Wigan's Cook of his half-time exchange with Guardiola.
The forward's argument is that he was simply defending himself against the fan's aggression, although he was also clearly angry and reacted to something, which he said was the spitting.
Although Fabian Delph's red-card was the sole dismissal of the tie, the game was not without plenty of niggle; Wigan receiving five yellow cards over the course of the ninety-minutes. "The emotions of football can sometimes get the better of fans and that was evident last night", he told BBC Breakfast.
However, it is understood the FA is satisfied that no misconduct took place during the interval.
"It is a massive result, but we have to stay classy in football, I don't like what I am seeing here".