Owen nodded home Nani's free-kick 16 minutes from time to ensure United did not join the other victims on a weekend of shock defeats.
Yet it was hardly a pleasing outcome for Ferguson, who would have hoped for better once Nani levelled Zat Knight's early effort but instead saw his team fall behind again thanks to Martin Petrov.
Bolton made the perfect start when they took the lead in the sixth minute after Knight latched on to Petrov's curling corner and back flicked the ball past Edwin van der Sar.
The United goalkeeper was forced to make a couple of vital interventions as Kevin Davies and Johan Elmander made their presence felt, with Jonny Evans not looking entirely comfortable, while at the other end, United's play was incisive and both Ryan Giggs and Wayne Rooney wasted decent chances.
United claimed the equaliser their midfield dominance deserved in the 23rd minute when Nani picked up the ball from his own half and after the Trotters defence backed off, the Portuguese winger had got to the edge of the area before he drilled an impressive shot past Jussi Jaaskelainen.
In fairness to Bolton, it was something of an aberration given how well they had done at closing down space around their penalty area and forcing United into pumping a succession of crosses into the box.
Petrov put Bolton back in front after 67 minutes, exploiting poor defensive work to step inside Park Ji-sung then rocket a shot past Van der Sar that flicked off John O'Shea.
The introduction of Federico Macheda did result in an opening for Dimitar Berbatov but it took Owen's deft near-post flick for the far corner from Nani's free-kick to bring United level.
A late onslaught was expected as United hunted the winner but it did not actually materialise, with Elmander, who had wasted an excellent chance to seal victory for Bolton before Owen scored, steering the final opportunity wide as well.
Source PA