The Tyrone attacker slipped his marker to plant the ball in the net and give the St Enda’s men the narrowest of wins at the end of a thriller.
A late Martin Penrose point appeared to have done it for Carrickmore, but they were left crestfallen by a late sucker punch, and forced to sift through the wreckage of a fourth defeat in a final since their last O’Neill Cup triumph in 2005.
They were level on five occasions in a fast-moving first half, with Joe McMahon edging the midfield battle against county colleague Conor Gormley.
Carrickmore were chasing the game until Penrose nudged them in front for the first time in the 29th minute
Earlier, Jason McAnulla, Jason McAnulla and Ronan O’Neill had all hit the target to keep Omagh ahead.
But Gormley started to emerge as a key figure once the central match-ups changed, inspiring his side with a wonderful long range point.
Carrickmore almost had a goal in the closing stages of the half when Penrose made a surging run and flicked the ball across to Niall Loughran, whose fisted effort was deflected on to a post by McMahon.
Wing-back Ruairi Loughran arrowed over his second point in stoppage-time to give Carrickmore a 0-8 to 0-6 interval lead.
Carrickmore missed another goal chance when wing-back Mickey Donaghy saw his shot superbly saved by Ryan Clarke, but they held on to the lead despite scoring just once in the third quarter.
Omagh closed the gap with scores from O’Neill and McMahon, who thumped over a long-range free, before inspirational centre-back Barry Tierney put them back in front with a wonderful surging run and point.
Carrickmore were reduced to 14 men in the 45th minute when defender Johnny Munroe received a second yellow card, but they went back in front when the excellent Penrose fired over two points from play.
The game had just slipped into time added on when Omagh launched one last desperate attack, which saw substitute Cathal McCarron pick out full-forward O’Neill, and he wriggled past two defenders to plant the ball in the net.
Scorers for Omagh: R O’Neill 1-4 (0-2f), C Grugan (2f), B Tierney 0-2 each, Joe McMahon, J McAnulla 0-1 each.
Scorers for Carrickmore: M Penrose 0-5 (2f), P McAleer 0-3, R Loughran 0-2, M Donaghy (f), C Gormley 0-1 each.
OMAGH: R Clarke, H Gallagher, Justin McMahon, S Mullan, C McLaughlin, B Tierney, C McMahon, Joe McMahon, C Grugan, A Grugan, J McAnulla, C O’Neill, C O’Donnell, R O’Neill, C Meyler.
Subs: M Flanagan for C O’Neill, C Starrs for McLaughlin, C McCarron for Meyler.
CARRICKMORE: P McCallan, M Slane, C McGurk, J Munroe, M Donaghy, B McLaughlin, R Loughran, N Loughran, C Gormley, F Magill, M Penrose, M Gallagher, P McAleer, M Donnelly, D Fox.
Subs: C Daly for Fox, P McMahon for Magill, B Daly for McAleer.
Referee: S Hurson (Galbally).