Mossley Hill play one level above MSB Woolton but the North West League side held out until Amy Hughes broke the deadlock 2 minutes before the break.
There was still just the only goal in it going into the dying minutes, when substitute Megan Brodie got Mossley’s second to seal the cup.
Mossley now must turn their attention to securing their Premier League status on Sunday and they have a tough fixture at Hull City, who are chasing the runners-up spot.
All three points are required by Mossley to have a chance of finishing outside the bottom two of Northern Division 1.
