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Harps got the second half off to a dream start when Eloka Asokuh met an Anothony Gorman header to level the scores.
And with the crowd cheering them on, play then swung from end to end with John O’Flynn finding the side netting for City and Kearney then firing over.
But Harps took the lead in the 72nd minute when Chris Breen capitalised on a mistake by goalkeeper Michael Devine to put the ball into an unguarded net.
City looked to be in real trouble but with six minutes left Damien Richardson’s side equalised as O’Flynn found the target after goalkeeper Gavin Cullen failed to cut out the ball.
Harps had the better chances in extra time with Jonathan Minnock crashing a free against the crossbar on 112 minutes.
But City then grabbed the winner to leave the Finn Park faithful stunned.
Finn Harps: Cullen, Asokuh, Minnock, Boyle, Bradley, Funston, Capper, McGrenaghan, Laughlin, McHugh, Gorman. Subs: Scoltalk for Boyle (41 mins), McGowan for Funston (78 mins)
Cork City: Devine, Murphy, O’Halloran, Coughlan, Murray, Fenn, O’Flynn, O’Callaghan, Gamble, Horgan, Kearney. Subs: O’Donovan for O’Halloran (70 mins), Behan for Fenn (84 mins).