Coasting at 2-0 up with 15 minutes to go thanks to an own goal by Zat Knight and Antonio Valencia's first for the club, United suddenly suffered a bout of the nerves after Matt Taylor reduced the arrears.
The confidence seemed to drain from the champions into Wanderers as Bolton piled on the late pressure.
Bolton seemed camped in the United half with substitute Ivan Klasnic inches wide with a shot and Gary Cahill heading straight at United goalkeeper Edwin van der Sar deep into injury time.
United had enjoyed the perfect start with a goal after five minutes.
Michael Carrick found Patrice Evra on the left and his cross from the near post saw Michael Owen's header from six yards bundled into his own net by Knight.
Owen should have added a second goal a minute later, but his free header from Ryan Giggs' right-wing cross from six yards went straight at Bolton goalkeeper Jussi Jaaskelainen.
Dimitar Berbatov's goal-bound volley went wide off Owen, while Valencia's shot from 25 yards out was turned behind by Jaaskelainen.
But United's second goal finally came after 33 minutes. A glorious cross-field move started when Giggs found Evra on the left.
Evra's ball into the centre was helped on by Owen to Valencia on the right and he worked a neat one-two with Gary Neville before scoring with a powerful right-foot shot from 12 yards.
United continued to dominate after the interval and Berbatov should have put the game beyond Bolton's reach in the 57th minute when his acrobatic volley from a Giggs cross was brilliantly saved by Jaaskelainen.
But United went to sleep in the 75th minute. Kevin Davies, whose physical presence caused United problems all afternoon, crossed from the left and Taylor soared above Evra at the far post to head home from six yards.