Spot kicks were required to separate the sides and it was the Rebels who edged through to the last four.
QUB and UU had already exited the competition before the quarter-finals, so St Mary’s were the last Belfast College standing.
Armagh’s representatives on the Ranch side made big contributions to the game, and all played their part.
Gavin McGilly’s side trailed the whole way through normal time, but a last gasp goal kept their hopes alive.
Clann Eireann’s Conor McConville pointed an early free, to match Shane Merritt’s opening score.
UCC bagged a goal through Cathal O’Mahony and Gavin McGilly’s side struggled to narrow that gap.
The goal was the difference at the break, with Billy Morgan’s Cork side ahead 1-3 to 0-3 at the interval.
Five was soon the difference, but a point from Crossmaglen attacker Dara O’Callaghan and Scotstown midfielder Michael McCarville helped dwindle the margin once again.
O’Callaghan had another big input before the end of normal time. He’s long ball in was taken by Matt Og McGleenan who blasted the ball to the net to force extra time.
O’Mahony edged UCC ahead but a huge score from Granemore’s Louis Hughes got St Mary’s back on level terms.
O’Callaghan slotted over a free to hand St Mary’s the lead for the first time, but they couldn’t hold the lead.
A late pointed free from O’Mahony force penalties as the teams finished all square, 1-10 to 1-10.
UCC keeper Dylan Foley was the hero as he saved spot kicks from Cormac Murphy, O’Callaghan and McConville.
It wasn’t to be for St Mary’s, but the Armagh lads involved, including manager Gavin McGilly, can hold their heads high.
Clann Eireann duo Danny Magee and McConville (0-1). both started the game, as did Mullaghbawn midfielder Cormac Smyth.
O’Callaghan (0-2) was introduced in the second half, while Clonmore’s Sean Quigley and Louis Hughes (0-1) also saw game time.