They were rightly angry about Bolton's first goal, a drive from Gary Speed from a tapped free-kick after Jose Reina had been wrongly penalised for handling outside his box. Television replays seemed to show otherwise.
But an Ivan Campo header soon after the break put Bolton in control, and they rarely looked likely to lose their grip on the points from that position.
Bolton kept an unchanged side, while Liverpool boss Rafael Benitez made four changes from the team which beat Galatasaray in the Champions League in midweek.
• Speed hails battling Bolton
Out went Daniel Agger, Peter Crouch, Fabio Aurelio and Luis Garcia, and in came Mohamed Sissoko, Sami Hyypia, John Arne Riise and Craig Bellamy.
England boss Steve McClaren was at the Reebok to watch the game and he got a better reception than Benitez.
The Liverpool boss had made no secret of his dislike for Bolton's style and the home fans let him know they were not too impressed with the views of the Anfield camp.
Liverpool's first chance came when Dirk Kuyt saw a header well saved by Jussi Jaaskelainen.
Then on 15 minutes Abdoulaye Faye was booked for hauling down Steven Gerrard, Benitez again venting his anger on the touchline.
Liverpool were unfortunate not to take the lead when Bellamy's cross from the left was headed out to Xabi Alonso, who struck an 18-yarder against a post and behind with Jaaskelainen beaten.
Then came the first flashpoint. Faye, already cautioned, caught Kuyt in the back of his head with an arm, but the referee chose to give the defender a lengthy warning than another card.
The Dutch striker sprinted to the dressing room for further treatment and returned with his hair caked in blood.
Within minutes Bolton were ahead, from a controversial free-kick awarded on a linesman's insistence that Reina had handled outside his box as he drop-kicked a clearance.
TV replays showed that the Spanish goalkeeper had released the ball from his hands just inside the area and kicked it outside.
Bolton took full advantage as Campo touched the free-kick to Speed and the Welshman's drive flashed into the net through a ruck of players.
Jaaskelainen made a fine block from a Gerrard drive, but Bolton finished the half by putting Liverpool under intense pressure from set pieces.
Two minutes into the second half Speed was booked for pulling back Pennant and two minutes later Kuyt was taken off to allow Crouch into the fray.
But Liverpool's task was made even harder on 50 minutes when Bolton went two ahead. Kevin Davies was allowed to fire in a cross from the right and Campo rose above Steve Finnan to see his header hit the bar and bounce down over the line.
Three long-range efforts from Alonso was all Liverpool could muster in response before Benitez took off the disappointing Pennant and sent on Luis Garcia on 58 minutes.
Crouch was booked for a two-footed lunge at Speed after 74 minutes and Liverpool sent on Bolo Zenden for Sissoko a minute later just before Bellamy wasted a decent chance created when Gerrard robbed Hunt.
Speed hails battling Bolton
Bolton veteran Gary Speed hailed his team-mates after they hustled and harried
their way to a 2-0 win over Liverpool at the Reebok Stadium.
Speed, making his 750th club appearance, told Sky Sports One: 'Liverpool are
a good footballing team, they were Champions League winners a season or so ago
and you can't let these players have time on the ball.
'We pressed them high up the pitch and got our just desserts.
'We've not conceded a goal at home yet and I'm sure people come here and
adapt accordingly, which gives us confidence.
'We've got to keep it going, we've given ourselves a base and got some points
in the bag.'
Manager Sam Allardyce was delighted by a typical Bolton performance to get the
victory.
'This performance was just as good as against Portsmouth because it was
against one of the big boys,' he added.
'The performance nullified them. We closed down, worked hard and had a
gameplan and we frustrated Liverpool for all of the game really.
'What half-chances they did get, people were prepared to die to stop the ball
going in the back of the net.
'Our opportunities were very few but we've taken them. We might have been a
bit fortunate with the free-kick but we've taken advantage of it.
'Our defensive quality as a team was outstanding today.'
Liverpool manager Rafael Benitez made no attempt to hide his
frustration and annoyance with the officiating.
'It's clear that a mistake has been made,' the Spaniard told
the club's Web site. 'Pepe let go of the ball inside the area
and then kicked it outside. The linesman was in a bad position.
'I knew at the time it was a mistake but what can you do?
'Every week we can talk about incidents but nothing changes.
It's annoying.'
Bolton Wanderers 2 - 0 Liverpool
