They saw off UCD in the decider at Connacht GAA Centre
St Mary's are Sigerson Cup champions for the first time since 1989.
They beat holders UCD by 0-13 to 2-6 in the decider at the Connacht GAA Centre in the 3pm throw in.
Newly dethroned champions UCD had reached the final by edging UL in Friday's semi final fixture, while St Mary's also progressed by a narrow margin against UCC. It bridged a 24 year gap since St Mary's had reached a final and also provided an opportunity to end a 28 year wait for third level glory.
St. Mary's Conor Meyler with Jack McCaffrey of UCD ©INPHO/Tommy Dickson
The Belfast college had conceded two goals in quick succession in their semi final against UCC, and that was repeated against UCD this afternoon.
Within three minutes of action, the Dublin university had scored a haul of 2-0 without reply through Colm Basquel who got the first. And the same player netted the second to leave St Mary's trailing by six points early on.
But just like against UCC, they inched their way back and with UCD struggling to add points to the two early goals, St Mary's were able to build a 0-9 to 2-1 lead at half time.
UCD did get five more points on the board in the second half but St Mary's were able to supply four of their own to just about hold on for a one point win and just their second ever Sigerson Cup win.
UCD still lead the way in terms of all time titles with 33, 11 clear of NUI Galway.