The former England striker came off the bench in the 71st minute and glanced home Nani's free kick three minutes later to put United second in the table - three points behind Chelsea and one above Arsenal.
Portugal winger Nani's superb solo goal had earlier canceled out the opener scored by Zat Knight, but Martin Petrov put United's northwest neighbor Bolton in the lead again with a deflected shot in the 67th minute.
It was Owen's third goal of the week, having scored twice against Scunthorpe in the League Cup on Wednesday, and helped United claim its third successive away draw.
Manager Alex Ferguson will be frustrated his side could not capitalize more on the slipups by rivals on Saturday - Chelsea lost 1-0 at Manchester City, and Arsenal was defeated 3-2 at home to West Bromwich Albion.
Bolton opened brightly and took the lead in the sixth minute when Petrov's left-wing corner was flicked in by center back Knight, who got to the ball just ahead of Jonny Evans.
Conceding that early goal sparked United into life and the visitors laid siege on Bolton's goal, with Wayne Rooney and Darren Fletcher forcing saves out of Jussi Jaaskelainen.
United deservedly equalized through Nani, who picked the ball up on halfway and set off on a run through the Bolton defense before shooting low into the corner from 20 yards.
United remained in charge but Bolton held out until half time and started the second half impressively.
Petrov fired just over from 25 yards and Bolton's physical front pairing of Kevin Davies and Johan Elmander gave United center backs Nemanja Vidic and Evans no peace.
The ineffective Rooney was taken off by Ferguson in the 61st and Bolton went ahead for the second time six minutes later. Petrov cut inside and saw his right-foot shot flick off the side of Fletcher and past goalkeeper Edwin van der Sar at his near post.
Owen was then introduced for Fletcher and made an immediate impact when he made a darting run to the near post and headed Nani's free kick off the far post.
Elmander had a chance to win the match for Bolton but the Sweden striker dragged an 84th-minute shot across the face of goal.
