A sensational result saw former City hero Uwe Rosler lead the Championship side to an incredible victory against the Citizens one season after they beat the Blues in the final.
Jordi Gomez and James Perch put Wigan 2-0 ahead by the 47th minute and managed to hold on after Samir Nasri gave City hope in the 68th.
Wigan will now play against Arsenal in the semi finals.
In the other FA Cup matches played today Hull City beat Sunderland 3-0 while Sheffield United triumphed over Charlton 2-0 and it means there will be a guaranteed underdog in the FA Cup final at Wembley. Sheffield United became the first third-tier team to reach the FA Cup semifinals since 2001.