Midfielders Mark Davies and Nigel Reo-Coker gave the home side a deserved 2-0 lead inside half-an-hour and although Craig Bellamy's seventh of the season reduced the deficit, Gretar Steinsson restored the two-goal cushion just five minutes into the second half.
The victory saw Wanderers move out of the bottom three with a performance full of desire and tenacity which, especially in the first half, had the visitors' looking at each other quizzically.
Manager Kenny Dalglish will also no doubt want answers to how a side with only one home win all season - and who have lost their last 10 against the Reds - could open up a usually reliable defence so easily.
Prior to this match only Premier League title-chasers Manchester City and Tottenham had scored three or more against Liverpool this season.
Worryingly for Dalglish, they have to face City at home on Wednesday in the second leg of the Carling Cup semi-final holding just a slender 1-0 lead.
If they defend as poorly as this the 16-year wait for a Wembley appearance may go on even longer.
Wanderers made it 10 points from their last six matches and manager Owen Coyle will hope this result will prove to be a turning point for his beleaguered side.
But after watching his players fail to break down Stoke last week - one of many struggles at Anfield - Dalglish has to find a way of lifting a team which has won just once in six league matches, collecting just six points.
Liverpool's excellent record against Bolton counted for little as early as the fourth minute when the home side took the lead.
Martin Skrtel stepped out to meet Chris Eagles' pass into David Ngog but the slightest of touches from the former Reds striker moved it on to Davies who charged into the penalty area to shoot low just inside Jose Reina's left-hand post.
Eagles should have made it 2-0 when he held off the challenge of Jose Enrique as he ran in from the touchline only to fire a cross-shot past the far post from a narrow angle.
Bellamy, playing up front alongside Andy Carroll, was by far Liverpool's biggest threat with his pace getting him behind the Wanderers defence on a number of occasions.
The Wales international had one shot blocked by David Wheater while Carroll, who began to link better with his partner as the match wore on, headed straight at Adam Bogdan from Steven Gerrard's crossfield pass.
After Maxi Rodriguez's penalty appeal for the ball hitting Zat Knight's arm was rejected Bolton all too easily carved open Liverpool's defence for a second time.
Eagles was again the instigator, coming off the right touchline to chip the ball over the centre-backs for Reo-Coker to stab home.
Carroll was coming into the game more and after one first-time pass sent Bellamy racing through to shoot at Bogdan his flick-on led to a goal.
His header from Reina's clearance sent the Welshman racing through and this time he cleverly clipped the ball past the Bolton goalkeeper.
Bogdan then saved well from Gerrard's shot before Reina batted away Martin Petrov's free-kick in first-half added time.
Liverpool's hopes of redressing the balance early in the second half were snuffed out after just five minutes when Wheater headed Petrov's corner back across goal and Steinsson slid a shot inside the post.
With 25 minutes to go Stewart Downing and Dirk Kuyt were sent on for Rodriguez and Charlie Adam in an attempt to rescue the situation.
The chances were still falling to Carroll though but his luck did not improve as he blazed over from Davies' mis-control in the penalty area before completely missing Downing's cut-back.
Defender Daniel Agger had come closer moments earlier when his long-range drive clipped the top of the crossbar.
Carroll, without a league goal since October 29, continued to labour in front of net, typified by his complete miskick from Downing's cut-back.
Liverpool's attacking in the closing stages became even more desperate but they rarely looked like threatening Bogdan.
A first win over the Reds since September 10 did wonders for Bolton's confidence, less so for Liverpool who are looking increasingly ragged by the week.