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.
As United have now conceded nine goals in five league games and trail leaders Chelsea by three points, it was not the best of weekends for them, nor an out-of-sorts Wayne Rooney, who was replaced by Federico Macheda half an hour from the end.
Saturday's results could not have worked out any better for United and the intent behind their attacking play was obvious from the first kick, but defensively they remain unconvincing. The absence of Rio Ferdinand with Wednesday's Champions League encounter with Valencia in mind was a further indication that all is not well with the England skipper. And without him, life continues to be a struggle.
A late goal at Fulham, two in injury-time at Everton and a Steven Gerrard brace against Liverpool last weekend when the Reds did not have a single shot of note in open play during the entire game is not a record to be proud of.
To that crime sheet can now be added Knight's back flick. The defender's third goal in as many years could not be described as conventional. But once Patrice Evra moved away from the far post he was supposed to be patrolling when Petrov curled over his corner, the target was wide enough for him to steer the ball into once he had escaped the attentions of Jonny Evans.
That United would score themselves was never really in doubt such was their dominance of possession in key midfield areas. The problem was whether they would concede again in the meantime. Edwin van der Sar was forced to make a couple of vital interventions as Kevin Davies and Johan Elmander made their presence felt, with Evans not looking entirely comfortable.
At the other end, United's play was incisive and both Giggs and Rooney wasted decent chances. The manner of the visitors' equaliser would have come as a disappointment to Owen Coyle. Nani deserved plenty of credit for his ambition as he set off racing towards the Bolton goal from inside his own half. However, the Trotters defence just kept inviting him to run and 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. It was a tactic United persevered with after the interval and eventually resulted in the substitution of an ineffective Rooney half an hour from the end.
Rooney's work rate could not be faulted on his first appearance away from Old Trafford since the storm erupted over his private life. But he does not threaten at the moment and now Owen has taken his tally to three in a week, compared to one for Rooney - from the penalty spot - all season, an interesting selection dilemma looms for Ferguson in Valencia on Wednesday.
Owen was not even on the pitch when Petrov put Bolton back in front, exploiting more poor defensive work to step inside Park then rocket a shot past Edwin van der Sar that flicked off John O'Shea.
The introduction of Federico Macheda did result in an opening for 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.