The 17-year old’s penalty in the 105th minute, coupled with a late goal from Isaac Buckley, completed the comeback after Will Patching’s superb free kick cancelled out Callum Lang’s opener.
City started on top and had a chance to take the lead in the opening five minutes. Nmecha latched onto a perfectly weighted through ball and chipped the onrushing Kelland Absalom, only to see his effort cleared off the line by Arnold Baxendale.
It was a fairly quiet first half following the early chance with both teams battling for the ball in midfield. Wigan’s Joshua Gregory rose highest from an Alex Lingard corner, but headed straight at Daniel Grimshaw in the only other notable chance of the first 30 minutes.
Jason Wilcox’s side dominated the possession in the first 45 minutes and created two chances as the first half came to a close. First, Nmecha headed over the crossbar from close range under heavy pressure from Luke Burke before Patching saw his free kick drift narrowly wide of the post with the last kick of the half.
The home side came firing out of the blocks after the restart and took the lead in the 50th minute. Callum Lang capitalized on a mistake at the back and fired past Grimshaw to give Wigan a one-goal advantage.
City responded well to going behind and drew level just 16 minutes later. Jacob Davenport was fouled on the edge of the area and Patching placed the resulting free kick into the back of the net, leaving Absalom rooted to the spot.
As time ticked by, the game became more open as both sides looked to snatch a winner late on. Wigan’s Josh Gregory dragged a shot wide of Grimshaw’s goal before substitute Buckley nearly won it with just a few minutes to spare.
First, Buckley rattled the upright with a ferocious shot and that was followed by the 17-year old fired over the crossbar from ten yards out after being played in by Rodney Kongolo.
Three minutes of added time were indicated at the end of the second half and both sides had a chance to seal progression during that time period.
Brahim Diaz came close for City but he couldn’t get a clean contact after Buckley pulled the ball back before Wigan had a chance to win it with almost the last kick of regulation time.
Alex Lingard swung a free kick into the six yard area and it was met by Thomas Powell, who saw his header saved by Grimshaw in the City goal to send the game into extra time.
The first period of extra time didn’t kick into action until a minimum of three minutes were indicated by the fourth official.
Shortly after the board went up, the hosts thought they had taken the lead for the second time in the game but Demeaco Duhaney showed great awareness to get back and clear off the line.
City pushed forward immediately after the clearance and their hard work was rewarded when referee Tom Nield awarded a penalty after Nmecha was brought down by Wigan goalkeeper Absalom.
The 17-year old brushed himself down and stepped up to take the spot kick, burying the penalty in the bottom corner to make it 2-1 to City.
Absalom atoned for his error with eight minutes to go by producing a fantastic save to prevent Brahim adding City’s third but he couldn’t do anything to deny Buckley in the 122nd minute.
The City substitute latched onto Nmecha’s excellent heel flick, which took out two defenders, and Buckley slotted the ball between the legs of Absalom to seal a place in the FA Youth Cup Quarter Final.