A 51st minute goal by Fermanagh's Ciaran Corrigan was the pivotal score for Paddy Tally's side who upset 13-man UCC at Connacht's GAA centre on Friday.
Crossmaglen's Oisin O'Neill hit 0-3 while Matthew Fitzpatrick's goal in the 17th minute helped the Belfast college lead 1-6 to 2-2 at the break.
St Mary's, champions in 1989, play holders UCD in Saturday's final.
UCD beat UL 1-10 to 0-11 in the day's second semi-final.
UCC hit early goals through Ian Maguire and Cathal Bambury but St Mary's rallied with points from O'Neill and Tyrone's Kieran McGeary.
Antrim forward Fitzpatrick's goal got them ahead and Corrigan palmed the ball to the net, after Cathal McShane's purposeful run, for a crucial score.
Corey Quinn put St Mary's two points ahead and they survived a late barrage of pressure from the Cork side, who had Adrian Spillane and Alan O'Donovan sent off late on.
St Mary's are through to a Sigerson Cup final for the first time since 1993 with a shock 2-7 to 2-6 win over UCC.