A nervy affair was brought to life after 16 minutes when a defensive error allowed Nikica Jelavic to fire home for the hosts, before QPR captain Joey Barton was shown a red card for lashing out at Tom Huddlestone.
Despite Hull's numerical advantage, Charlie Austin - who failed a medical at the KC Stadium back in 2013 - was on hand to restore parity just before half-time, flicking home a teasing cross from Matt Phillips.
A second half largely devoid of quality seemed set to ensure QPR claimed an unlikely point, before N'Doye fired home at the death to earn his side a second consecutive league win.
It is the first time Hull, who are now up to 15th, have sealed back-to-back league victories since September 2013, handing a massive boost to boss Steve Bruce.
QPR, meanwhile, are above the relegation zone on goal difference alone ahead of home games against Arsenal and Tottenham.
Both teams came into the match on the back of morale-boosting 2-0 victories before the FA Cup weekend, but it was nevertheless a cagey opening 10 minutes at the KC Stadium.
That all changed when Hull, who fielded the same XI from their win over Aston Villa, were gifted a breakthrough.
A high ball into the box from Huddlestone was poorly cleared by the head of Steven Caulker, allowing Jelavic to lash a shot home with aplomb.
QPR's Darnell Furlong nearly restored parity four minutes later, but the 19-year-old was denied a goal on his senior debut when his header was superbly tipped over by Allan McGregor.
Jake Livermore then fired over the crossbar, before Furlong - son of former QPR striker Paul - found himself at the centre of the action again after 32 minutes. His late challenge on David Meyler sparked a fracas, eventually resulting in QPR captain Barton being shown a red card for an apparent punch on Huddlestone.
An eventful first half took another twist six minutes before half-time, when Austin rose highest to flick home an unlikely equaliser following Phillips' fine cross.
Huddlestone should have put his side back in front on the stroke of the interval, but he rifled a shot just wide.
The hosts introduced Gaston Ramirez just after half-time in an attempt to make their numerical advantage count, but they could not find another breakthrough.
A fragmented display posed few problems for the QPR defence for much of the second half, and goalkeeper Rob Green was largely untroubled.
QPR looked to have done enough to secure a draw, but N'Doye sealed the win in the last minute of the game, first forcing a superb save from Green with a powered header, before popping up again just a few seconds later to convert a Robbie Brady cross.
