Garbally College head coach Ronan Flanagan said he never lost faith in his side as Niall Collins' late try snatched glory at the Sportsground.
Winger Collins touched down with two minutes remaining and the competition's most decorated side held on to secure a 42nd Junior Cup.
"It was an unbelievable finish - it was heart-stopping there at the end. I still believed in the last five minutes, we kept knocking on the door and we got there in the end," said Flanagan.
Garbally trailed 10-5 at half-time after Luke Kelly cancelled out Patrick Grehan's try.
But flanker John Claffey touched down after half-time and Collins had the final say.
It only took them seven minutes to get their first score, a try from Grehan after a powerful effort in the scrum.
Kelly's try and Darragh Hanrahan's boot put 'The Jes' 10-5 up at half-time, but Claffey and Collins ran in the crucial tries for the Ballinasloe side.
Garbally College - T Fitzpatrick; P Flanagan, S Jennings, J Carry, N Collins; C Tracey (C Goode 54), M Devine (C Finn 41); S Egan, O Dooley, J Curley (C Silke 41); M Mitchell, P Galvin; J Claffey, O McCormack, P Grehan.
Coláiste Iognáid - M O Griofa; H Devlin, N Hanahoe, J Power, L Hurson; D Hanrahan, L Kelly; L Solan, T Gilanders, G Lally; L Smyth, B Kelly; O Kelly, D McCormack, G Hill.
Ref - S Gregory.