St. Eunan's led 0-7 to 0-6 at half time.
After the break the Letterkenny side appeared to take the upper hand after Eoin McGettigan was sent-off but Naomh Conaill then stepped up their game and having drawn level at 0-8 apiece Dermot Molloy then scored a point to give the Glenties side the lead.
Caolan Ward equalised for St. Eunan's but Naomh Conaill, whose subs made a big impact, then restored a one point lead through Johnny McLoone to make it 0-10 to 0-9.
Aaron Thompson was in the right place to increase the lead for Naomh Conaill and leave them 0-11 to 0-9 with two minutes left.
Rory Carr reduced the deficit and St. Eunan's pressed hard for an equaliser as they tried to force a replay. Conal Dunne missed a late chance for the O'Donnell Park side.
But Naomh Conaill held on for a memorable win and a third title as they dethroned the champions.
It finished, Naomh Conaill 0-11, St. Eunan's 0-10.