Michael Newman provided the winning score, but it was the disciplined team performance that will please manager John Divilly most as he watched his side overturn a three-point half-time deficit.
Queen’s led 0-3 to 0-1 on the quarter hour mark but three Maynooth points without reply had them ahead for the first time on 26 minutes.
The game’s only goal — scored by Queen’s Niall McKenna had them in front 1-5 to 0-5 at the break.
The sides were soon level with Newman, Paul Calahane and James Califf all pointing for Maynooth before Cian Mullins put them ahead on 46 minutes.
The game was nip and tuck to the finish and extra time loomed until Newman’s stole it late for the visitors.
NUIM: S Connolly; K O’Brien, K Lynch, D Dalton; T Moolick, J McDermott, C Brophy (0-1); C Berrigan (0-2), C Mullins (0-1); J Califf (0-3, 2f), G McIntyre, S Denvir; M Newman (0-4, 3f), P Calahane (0-1f), D Quinn.
Subs: P O Griofa for G McEntyre, S Fahy (0-1) for S Denvir, F Toolan for C Berrigan.
QUB: M Jackson; N McGovern, B Cox, O Costello; T Hanna, P McGuigan, S Finch; M Sweeney, S Burke (0-1); J O’Reilly, J Kielt (0-3f), A Murnin; C Rafferty (0-1), N McKenna (1-1), D O’Hare (0-2f).
Subs: M Armstrong (0-1) for A Murnin, E Clarke for J Kielt, J Kielt for M Armstrong.
Referee: P Hughes (Armagh).