City thought they had grabbed a point when Craig Bellamy steered home their third leveller in the final minute. But up popped Owen, just as he said he would, with virtually the final kick of the game to leave the Blues on their knees.
United had taken the lead after just two minutes through Wayne Rooney, but a catastrophic error from Ben Foster allowed Carlos Tevez to set up Gareth Barry, who made it 1-1.
Darren Fletcher headed home a Ryan Giggs cross seven minutes after the break to put United ahead for a second time, but Bellamy equalised when he cut inside John O'Shea and fired home a sensational 20-yarder.
Fletcher then headed United ahead once again from a Giggs free-kick, only for Bellamy to level again in the final minute of normal time following a lazy misplaced pass from Rio Ferdinand.
The goal looked to have earned City a point, but with visiting manager Mark Hughes screaming for the final whistle, Owen latched onto a through-ball from the irrepressible Giggs before stabbing home the winner.