Town opened the scoring when Jack Richards finished a move started by a great free kick from Dylan Glass.
Athletic keeper Jay Foulds could only parry to Matty Johnson who headed forward and captain Richards scored.
Johnson was on hand to add Town’s second before Athletic pulled a goal back.
But in injury time man of the match John Edgerton scored Town’s third to seal the win.
Ashton Town and Ashton Athletic Development squad met in the Wigan Cup Final on Wednesday night, with Town coming out on top 3-1 at Garswood United.