At the final whistle, Wigan fans ran onto the pitch to celebrate with their players.
But Aguero lashed out at one supporter after he was approached as he headed towards the tunnel.
The Argentine striker struck the fan with his right arm but was restrained by Wigan defender Cheyenne Dunkley and a member of City’s coaching staff as he tried to get closer to the man.
’ Wigan boss Paul Cook said on Aguero’s altercation: ‘It’s not right, is it? It’s not correct, Player safety is paramount,
City are also facing a charge from the Football Association after their supporters rioted in the stands after the defeat to Wigan.
A heavy police presence was required to contain the agitated City fans, who threw an advertising hoarding towards the pitch which struck an officer.