UCC had two men sent off, but still battled their way into a fourth final in five years in Belfast.
Billy Morgan's side were never behind against Maynooth, but they lost their Cork playmaker Alan Cronin to an off-the-ball straight red card offence after 39 minutes and Michael Quinlivan went 10 minutes later after a yellow card was quickly followed by a black.
Maynooth played some nice football against the wind in the first half, but made poor use of it in the second, while UCC played with a lot of heart despite their red cards.
UCC refused to buckle and in Kerry forward Conor Cox they had the outstanding player on show.
He hit 0-7, including four brilliant points into a gale-force wind in the second-half.
Paul Geaney scored 1-3 for the Cork side, all in the first-half, but it was Cox's gutsy points into the wind which were the real match-winners.
Maynooth were the team with the star names and All-Ireland winners Paddy McBrearty and Michael Darragh Macauley were influential for them.
McBrearty was their top scorer with 0-6, including three from play over the hour, and Macauley won and carried a lot of ball. Pacey Meath forward Eamonn Wallace also scored two first-half points.
However, there was more togetherness about UCC and Paul Geaney got a decisive goal in the seventh minute.
The Maynooth goalkeeper's kick-out held up in the wind before Cronin won possession and fed Geaney who took one solo before burying the ball back past Mark Donnellan.
It gave UCC a precious cushion and they still led by 1-6 to 0-6 at half-time.
Maynooth had closed the deficit to two points when Cronin was given his straight red as play was being held up at the other end of the pitch for an injury to Wallace.
The Cork player held his head in his hands in disbelief at the dismissal, which rules him out of today's Sigerson Cup final.
McBrearty showed great leadership to step up and hit two monster frees to draw Maynooth level on 41 minutes – the first time the sides had been level since the sixth minute.
A man down, their lead gone and facing into a hellish breeze, UCC looked to have everything against them, but they dropped bodies back and were smart on the ball, picking their runs cleverly.
Defenders David Culhane and Tom Clancy broke forward to score important points, with Cox and substitute Sean Kiely adding the final touches to an impressive victory.
Scorers – UCC: C Cox 0-7 (4fs), P Geaney 1-3, D Culhane, T Clancy, M Quinlivan, S Kiely 0-1 each. NUI Maynooth: P McBrearty 0-6 (3fs), E Wallace, P Brophy (1f) 0-2 each, P Cribben, P Faulkner 0-1 each.
UCC – B Kelly; D Culhane, E O'Mahony, F McNamara; T Clancy, C Dornan, B Sheehan; D Nation, I McGuire; L Connolly, A Cronin, B O'Driscoll; C Cox, M Quinlivan, P Geaney. Subs: S Kiely for Nation (45), S Keane for Connolly (45).
NUI MAYNOOTH – M Donnellan; C O'Shea, P Faulkner, D Hyland; E Lowdnes, F Conway, J Gonoud; MD Macauley, D Kelly; P Cribben, P Brophy, E Wallace; D Duke, P McBrearty, R Kennedy. Subs: E Mullan for O'Shea (23), S Mattimoe for Kennedy (38), D McNicholas for Kelly (51), F Toolan for Duke (58).
REF – B Cassidy (Derry)