A combination of work-rate, commitment and a sharp-eyed official allowed Sam Allardyce's side to muscle their way to victory.
A controversial first-half free-kick awarded against Jose Reina proved the turning point.
Gary Speed marked his 750th club appearance by firing home and Bolton never looked back.
Another linesman's intervention - this time a correct one - ruled Ivan Campo's second-half header crossed the line.
Despite winning ten corners and having 13 goal attempts, Liverpool couldn't end their dreadful scoring record away from Anfield.
They've yet to score an away goal in the Premiership from open play. And Benitez's decision to match Bolton's 4-5-1 formation backfired.
For the 94th successive game he changed his starting line-up with four alterations from the side that beat Galatasaray.
Opposite number Allardyce has a reputation as a tinker-man. But for only the third time in 53 matches he stuck with the same starting 11.
With Speed, Campo, Abdoulaye Meite and Jussi Jaaskelainen in imperious form, the Lancastrians may just have deserved all three points.
An agitated Benitez was like a jack-in-the-box in the early stages.
He berated the linesman for not spotting a blatant offside against Nicolas Anelka, protested at a Kevin Davies challenge on John Arne Riise and harangued his players for not closing down Kevin Nolan at a free-kick - Benitez just couldn't sit still.
He was also on his feet when Dirk Kuyt headed a Steven Gerrard free-kick goalwards. But Jaaskelainen, a hero in the 1-0 win over Portsmouth, produced a flying save, using his fists to beat the ball away.
Ex-Liverpool star Anelka should have done better after a slip by Sami Hyypia. But the Finn chased back to snuff out the danger with Anelka breaking into the penalty area.
Liverpool created another good chance after 20 minutes. Craig Bellamy's cross was only cleared to Xabi Alonso lurking 20 yards out and the Spaniard's rasping low shot struck an upright with Jaaskelainen well beaten.
Benitez went ballistic again after Abdoulaye Faye headed the back of Kuyt's head. Already booked for an earlier challenge on Gerrard, it was fortunate for the Senegalese defender that Mr Dowd viewed his latest intervention as accidental.
Benitez clearly indicated he believed the African had used his elbow as Kuyt disappeared for stitches.
It wasn't difficult to gauge Benitez's mood after Speed drilled Wanderers into the lead.
Reina was adjudged to have cleared the ball outside his area by an eagle-eyed linesman. Television replays suggested the ball was just inside the keeper's territory.
Speed and Campo stood over the free-kick, before the 37-year-old smashed a low left-foot shot through the wall for his second goal of the season.
Speed produced another telling contribution after 34 minutes. He showed great endeavour to chase back and deny Jermaine Pennant a clear shooting opportunity after the ball broke to the ex Arsenal starlet off a Wanderers defender.
Another Jaaskelainen intervention kept Bolton in front at half-time. Steve Finnan's cross was knocked back into Gerrard's path by Bellamy but the Wanderers goalkeeper again punched clear the England star's stinging shot.
Liverpool were at their best in the opening period of the second half but Campo's header from a Davies cross knocked the stuffing out of the Merseysiders.