Sergio Aguero was attacked by a Wigan fan during a pitch invasion after Manchester City were sensationally dumped out of the FA Cup.
The Premier League leaders were stunned by the League One side in the fifth round.
The encounter came to life on the stroke of half-time after Fabian Delph was dismissed for a reckless challenge.
It saw Pep Guardiola clash with Paul Cook on the touchline before the spat continued down the tunnel.
Will Grigg then gave Wigan the lead after a Kyle Walker mistake and they held on until full-time.
The supporter threw a punch at Aguero and the City striker had to be restrained when he tried to retaliate.
Some Latics fans ran to taunt the City fans, who responded by ripping off parts of the advertising hoardings and throwing them onto the pitch.
The City supporters also threw missiles onto the pitch and both clubs could be in trouble with the FA over the crowd disturbances.
Pep Guardiola claimed he did not see Aguero being attacked and it is understood City will speak to Wigan to ask why they could not protect their players better.
“I was in the locker room,” said the City boss. “I did not see it.”
Aguero was initially restrained by Wigan defender Chey Dunckley and a member of the City backroom staff.
But clearly incensed by the incident, Aguero tried to get back at the supporter before being led off the pitch.
It wasn’t the only unsavoury incident at the final whistle as Manchester City fans also clashed with stewards.
Members of the travelling contingent ripped down signs in their anger, and launching them down onto the pitch.
Wigan chairman David Sharpe condemned the pitch invasion, saying: “It’s not nice to see. Football is emotional, that’s what it does to fans. But I don’t like to see this at the end of the game.
“It’s a massive result, but we have to stay classy in football. I didn’t like what I’ve seen here.”
A number of signs were torn down and thrown, while plastic bottles were also tossed from the stands.
Fans at the front of the stand also became embroiled in angry scenes with both police and match stewards.
Guardiola and Wigan boss Paul Cook angrily clashed three times over Fabian Delph’s sending off just before half-time and the pair had to be separated in the tunnel.
Guardiola was furious because he felt Cook helped persuade referee Anthony Taylor to dismiss Delph for his reckless lunge at Max Power when the official initially produced a yellow card.
Cook played down his involvement in Delph’s sending off, which rules him out of Sunday’s Carabao Cup Final.
“I wasn’t refereeing the game,” he said. “I can assure you of that. There were four people there with the fourth official.
“Others in the ground obviously deemed it to be a red card. The conversation about the game shouldn’t be about that. It’s a great night for Wigan Athletic and one we should enjoy.”
Guardiola was also reticent about his furious row with Cook and tried to play down their clash.
“It was a red card,” said the City boss. “The referee decided what he decided. I’m not here to judge. It could be a red card.
“If you want to ask me about football, ask me. Nothing happened in the tunnel. He was just stating his position, that’s all.
“They had one shot on target and we created lots, but football in the end is about the result and I congratulate Wigan.”
Will Grigg bagged the winner 11 minutes from time to earn Wigan a third quarter-final in six seasons at home to Southampton.
“When the draw was made, it was like we weren’t in it,” said Cook.
“I’m sure Southampton are as shocked as we are.”
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