The Spanish striker came off the bench in the 65th minute but was a largely peripheral figure until he latched on to Lee McCulloch's flick in the final minute and steered a low shot under goalkeeper Ivan Randelovic.
Rangers had struggled to retain the ball and often their composure in the face of some fierce physical play from the Serbian side.
But with a potential £10million pay day looming from earning a place in the group stages of Europe's premier club competition, the home side timed their assault on the visiting goal to perfection.
Gers boss Walter Smith had opted to leave Kris Boyd on the bench in favour of a 4-3-3 formation with Jean-Claude Darcheville operating as a lone central striker.
But for all the energy and commitment from the Frenchman, he was too often isolated in attack and the home side rarely threatened.
The visitors came closest to opening the scoring in the first half when Filip Djordjevic latched on to a long clearance from Ivan Randelovic only to ripple the top of the net with a speculative looping shot from 35 yards.
On the stroke of half-time both sets of players became embroiled in a flare up after Rangers refused to put the ball out of play, but the referee - who had already booked three visiting players in quick succession - surprisingly decided to take no action.
After the interval the game followed a similar pattern with Rangers seeing plenty of the ball in the midfield area without really looking dangerous in the final third.
Novo came on for Darcheville with 25 minutes remaining, but it was fellow substitute Daniel Cousin who looked more capable of finding the winner as he rifled a 25-yard shot over the crossbar from a central position.
Barry Ferguson then drilled a shot from an acute angle into the side-netting after forcing his way past a resolute defence, before Novo came up with the decisive moment in the final minute of regulation play.