Castletown Geoghegan had looked in control just moments from time.
Clonkill are Slevin Coaches Westmeath Senior Hurling champions for a record 17th time.
Pat O'Toole's side secured their third successive crown by defeating Castletown Geoghegan by 3-16 to 2-16 after extra time in Mullingar yesterday.
Castletown had been on course for victory but a goal three minutes into injury time from Jordy Smyth sent the game into extra-time.
Niall Mitchell, who was returning from a shoulder injury, also netted in extra-time to secure a three-point victory for the men in green and gold.
Clonkill captain Brendan Murtagh became the first player to ever lift the Westmeath Examiner Cup three times as skipper and he says it was a special moment:
Their manager Pat O'Toole spoke with Gerry Russell after the game: