Owen, a 70th minute replacement for Darren Fletcher, scored with a clinical header after Martin Petrov's strike had appeared to set Bolton on course for victory.
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United had been given a tremendous incentive to claim all three points at the Reebok with title rivals Chelsea and Arsenal both losing 24 hours earlier.
But if Sir Alex Ferguson's players arrived at the Reebok expecting victory to be a formality, they would have been shaken out of their complacency by Zat Knight's sixth minute opener.
Not only did the goal give Bolton the lead, it once again highlighted United's current defensive frailties. Ironically, Rio Ferdinand watched the game from the stands having been omitted by Ferguson.
In the first instance, Knight easily outjumped Jonny Evans to flick Petrov's cross goalwards - not the first time Evans has been beaten in the air this season.
But with Patrice Evra abandoning his position on the far post, Knight's flicked volley was left to creep into the net beyond the helpless Edwin van der Sar.
United at least reacted positively, but Rooney once again looked a shadow of his former self and the creativity was left to Nani and Dimitar Berbatov.
Jussi Jaaskelainin was surprisingly underworked in the Bolton goal until Nani equalised on 24 minutes with a stunning solo strike.
It was a goal more in keeping with Cristiano Ronaldo than Nani, but the Portuguese winger displayed his growing confidence by sprinting from the halfway line and outpacing three defenders before beating Jaaskelainen from 20 yards.
At 1-1, United began to dominate possession, but chances remained limited and it was the home side who went closest to adding to the scoring before half-time when Johan Elmander beat Nemanja Vidic and had his shot well saved by Van der Sar.
United were lacking energy, despite Ferguson having rested all of his starting XI against Scunthorpe in midweek.
The malaise was clearly affecting Rooney and, eight minutes after Ryan Giggs limped off with a thigh injury, the England forward was replaced by Federico Macheda. Rooney was then shown nursing a gashed ankle on the bench.
Moments later, Bolton punished United by re-taking the lead through former Manchester City winger Petrov.
The Bulgarian was fed by Elmander and he turned Ji-sung Park before guiding a deflected right-foot shot into the net from six yards.
United bounced back again, though, when Owen made it three goals in two days with a header from Nani's 74th minute free-kick - four minutes after replacing Fletcher.
The lively Elmander went close for Bolton in the closing stages, but neither side could snatch the winner.
Source: Telegraph
Source: Telegraph