The Light Blues recovered the concession of an early Richie Lane try to hit back through the boot of scrum half Conor Murray, who comfortably converted two left-sided penalties, before hooker Mike Sherry scrambled over for an injury-time try.
But, fired up by the sending-off of young lock Ian Nagle for punching, Cork Con rallied superbly and took the game to their Munster rivals in the final quarter, edging ahead through a superb solo try from out-half Daragh Lyons and full-back Scott Deasy put the final nail in the coffin with a late penalty.
It was Garryowen's second defeat to Cork Con in an All-Ireland final in three years - they were also bettered in the 2008 AIB League decider - and a bitter pill for Paul Cunningham's side to swallow.
Unfortunately for Cunningham, that red card decision proved decisive in the end for all the wrong reasons.
"You don't like losing finals, no matter what they're in. Con played exceptionally well at the start of the match - we did well to be just five points down after about 20 minutes, it could have been more," he told IrishRugby.ie.
"We got ourselves into the game, got ourselves into the lead with the two penalties and scored right on half-time.
"Arguably their sending-off was the worst thing to happen for us, would you believe, because it galvanised them and gave them something to target and something to build themselves up around.
"We didn't deal with that. At the start of the second half we started reasonably well but Con just built and built and we just didn't handle it."
Garryowen sit second-from-bottom in AIB League Division 1A and will have to regroup quickly as they play a re-fixed game at home to Dolphin next Sunday.
After a difficult start to the season, there have been more encouraging signs for the Garryowen management in recent weeks and although this loss is a setback, they did show some glimpses of their best form in Athlone.
"It took us some time to find our feet but when we did, we were a match for Con - there's no question about that," admitted Cunningham.
"We got our lead before half-time through sheer will as much as anything else. Going in at half-time we were in good shape.
"When you lose a man, sometimes it can galvanise a team and that's what it did with Con particularly. I don't think we did anything different in the second half, they just galvanised around that and it was a late score to win it."
Commenting on league matters, Cunningham added: "We've got a very tough job next week against Dolphin. That's going to take a huge effort after the disappointment of today. A lot of tough work.
"We have to secure our league position, that's the critical thing at the moment."
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