It took over two and a half hours and all ten spot kicks for the visitors to eventually sink the UCC ship, with Jake Corrigan's penalty finally ending it.
Under clear blue skies both sides struggled to get a foot in the game early on, and Darragh Lucy's miscued volley from Cian Murphy's deep cross was the hosts' only early chance. At the other end Chris McIlloaine almost managed to squeak one inside the far post from a corner before Charlie Bornemann had to have his angles right to gather John McKeown's cross-come-shot.
McKeown was profiting on some sloppy fouls by the home team and putting in some dangerous free-kicks; Darragh Gannon inches away from applying an almost certain finishing touch at the back post before half-time.
UCC's indiscipline in their own territory was gifting the visitors some golden opportunities, and only a fine save by Bornemann denied McKeown from opening the scoring 36 minutes in with a driven set piece.
Maynooth switched to a more aerial plan in the second period, trying to catch UCC's defence on the turn with mixed success; one such attack caused some nervous moments in the home defence as Bornemann didn't properly clear a Sean Noble cross, and a few key blocks denied McKeown and Stephen Dunne getting efforts in.
The Leesiders had their best chance to take the lead about 20 minutes from time, when Sean O'Callaghan's cross from the volley found Daniel Pender, whose volley was intuitively scooped over by Michael Kelly in the Maynooth goal.
Andy Gannon could have counted himself lucky not to have conceded a penalty five minutes from regular time, as his hand appeared to stop the ball during a slide tackle to deny Dylan Kavanagh a chance at goal while moments later McLoughlin bailed out his keeper by heading Jake Corrigan's lob off the line with Bornemann stranded.
It should have mattered little however, as with seconds remaining Dunne's inch-perfect cross was headed just over by substitute Ciarán Ryan from six yards out.
NUI Maynooth picked up from where they left off in extra time, and UCC keeper Bornemann was again called into action to deny Corrigan's powerful effort with a strong left hand.
However that was the extra period's only real chance, and after a missed penalty on each side, Daniel Pender put his spot kick wide to setup Corrigan to secure Maynooth's place in the semi-final.
Joining them in today's semi-final will be UCD who also took penalties to defeat Queens University at the farm. The University of Limerick and Trinity play in the second semi with UL triumphing 2-1 in the Shannonside derby, while a late Ronan Hanaphy goal secured Trinity's place ahead of Dublin rivals DCU.