Aston Villa moved into fifth spot when Emile Heskey's late header earned them a 2-1 victory at Wolverhampton Wanderers in Gerard Houllier's first league match in charge of the midlands club while Stoke City won 2-1 at Newcastle United to move out of the bottom three after trailing at half-time.
Nani's audacious dribble from the halfway line cancelled out an early goal by defender Zat Knight and, after Martin Petrov had restored Bolton's lead, Owen came off the bench to rescue Sir Alex Ferguson's side with his 200th goal in English football.
United's third consecutive away draw of the season meant they missed the chance to take full advantage of Chelsea's 1-0 defeat at Manchester City on Saturday and Arsenal's surprising 3-2 home loss to West Bromwich Albion.
Champions Chelsea have 15 points from six games with United on 12. Arsenal and City have 11 points with Villa on 10.
United's struggle completed an unpredictable weekend in England's top flight and left Ferguson frustrated.
"Teams drop points when you don't expect it," he told United's website. "That's what the Premier League is like.
"Away from home we've scored seven goals and we've only taken three points. But we must take credit coming back again. Being behind twice away from home is not easy to come back from. It shows character."
United have dominated near neighbours Bolton in recent years, winning 10 of their last 11 meetings, but they were rocked after six minutes when Knight shot past Edwin van der Sar from close range.
The visitors were level after 23 minutes when Nani took possession near the halfway line and set off towards Bolton's goal. After ghosting past three defenders, the Portuguese winger angled a shot past Jussi Jaaskelainen.
Wayne Rooney, playing his first away game since revelations about his private life were plastered across the tabloids, endured another quiet match and was substituted after the break by Federico Macheda, suffering a slight ankle knock.
The England striker has managed just one goal for United since March and that came from the penalty spot against West Ham United this month.
Bolton regained the lead in the 67th minute with a sweeping move which ended with Johan Elmander feeding former Manchester City player Petrov to fire in a shot that deflected off Darren Fletcher and inside the post.
Elmander wasted a glorious chance to make it 3-1 and Bolton paid the price when Nani's teasing free-kick was glanced in by Owen for his first league goal of the season to reach a notable career landmark.
"Scoring has always been a part of my career, and it's always nice to score goals, but it's tinged with disappointment at not getting the win," Owen said.
Houllier, who witnessed many of Owen's goals while manager of Liverpool, was full of praise for the often maligned Heskey, another player who thrived under him at Anfield.
Heskey's thumping header from Ashley Young's cross after 88 minutes gave Villa the points after Villa had seen an early lead given to them by Stewart Downing cancelled out by Matt Jarvis.
"Everybody loves Emile at the club," Houllier told Villa's website. "He is a good team-mate and what he needs is to keep believing in himself."
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