Nenagh took the lead through a Jake Morris penalty in the first half and maintained that lead at half-time.
Wilton struck back early in the second half to level the score before Barry Coffey restored Nenagh's lead.
The Cork outfit brought it back to 2-2 with about 15 minutes of normal time left.
Dylan Burke was the hero of the day as his extra time goal gave Nenagh AFC a 3-2 win.
