However, the victory was marred by ugly scenes at the final whistle, with fans racing onto the pitch and appearing to taunt the City players, leading to Aguero lashing out at one fan.
Objects - including an advertising hoarding - were thrown at police and stewards from the Man City end during the angry post-match scenes, and Wigan chairman David Sharpe confirmed that the club will launch an investigation into the incidents.
"The emotions of football can sometimes get the better of fans and that was evident last night. I don't like to see what happened at the end of the game," Sharpe told BBC Breakfast.
"We'll have to look into it properly with the FA and the authorities over what was going on, but it looks like both City and Wigan fans weren't being too pleasant to each other, and there was damage to the stadium.
"But that can be emotion of supporters sometimes. Things can get carried away. We've got to remain classy in certain situations and that's the feeling we're taking from last night. I don't think it will detract from our victory - not one bit. I think people know how football is and what fans can do in a certain moment, they can get carried away.
"I think the main story is Wigan beating Man City, who were on for the quadruple. They're favourites for the Premier League, the Champions League - and a League One club has just knocked them out of the FA Cup."