With two of their possible title rivals falling to defeat on Saturday, United spied the chance to make inroads on Chelsea's lead but could only close to within three points of the champions after twice going behind to a spirited Bolton side.
Zat Knight put Bolton ahead after only six minutes when he produced a wonderful flick to score from a corner, before Nani equalised on 23 minutes when finishing off a lovely solo run with a low finish into the far corner.
After both Ryan Giggs and Wayne Rooney had been withdrawn due to fitness concerns, Martin Petrov saw his shot deflect off Darren Fletcher and past Edwin van der Sar. However, Owen was introduced from the bench to score his 200th career goal.
Heskey has been much maligned during his time at Villa but scored his second goal in two games under Houllier - in the Frenchman's first league game in charge - when producing a fantastic header after 89 minutes.
Stewart Downing had given Villa the lead in the first half when converting from a cross from Marc Albrighton, before Matt Jarvis saw a cross into the box evade team-mates and Villa goalkeeper Brad Friedel before nestling in the net after 61 minutes.
Kevin Nolan's 43rd-minute penalty had given the Magpies a deserved half-time lead, but Stoke responded after the break and were back on terms with 67 minutes gone when Sunderland old boy Kenwyne Jones, who had earlier hit both the post and the bar, headed home from close range.