A late header from Igor Biscan gave Liverpool an unlikely three points and took the Reds within a point of neighbours Everton in the race for the Champions League.
The much-maligned Croatian stooped at the back post to meet Djimi Traore's 85th minute cross to rescue a desperately poor Liverpool performance.
Reds boss Rafa Benitez rewarded tough-tackling youngster John Welsh with his first Premiership start following a series of impressive performances at England Under-21 level.
Scott Carson replaced Jerzy Dudek in goal and Mauricio Pellegrino kept his place ahead of Sami Hyypia following a brilliant derby display. Biscan, Traore and Antonio Nunez were all injury-enforced additions to the starting line-up.
Fernando Morientes was confined to the bench despite an early recovery from a groin injury, leaving little Luis Garcia leading the front-line, to be supported by skipper Steven Gerrard.
Sam Allardyce's high-flying team of over-achievers came to Anfield in the hope of leapfrogging the Reds in the table as they bid to secure Champions League football for the first time in their history.
Controversial on-loan star El-Hadji Diouf was denied the chance to play against his current employers due both to suspension and a clause in the loan deal, but other than him the visitors were at full-strength.
Bolton, willed on by a buoyant army of travelling Lancastrians, had a chance to open the scoring after just four minutes when Ricardo Gardener beat Carson to a well-struck corner.
In fact the visitors started much the brighter, passing with confidence as a disjointed Liverpool side struggled to find a pattern.
A magnificent save from Carson then denied Stelios Giannakopoulos' sweetly struck half-volley as Wanderers laid siege to the youngster's goal.
The game finally settled, but Liverpool and their isolated skipper Gerrard still struggled to impose themselves on proceedings and, watching from the directors' box, Big Sam looked delighted with his troops' early showing.
The Kop yelled for a penalty on 20-minutes when John Arne Riise appeared to be dragged down by Nicky Hunt, but referee Steve Bennett didn't spot the incident.
Further confusion in the Reds defence saw Jamie Carragher nod past the on-rushing Carson, but luckily their blushes were spared as Giannakopoulos failed to reach the loose ball.
On 26 minutes Gerrard finally asserted some impact on the game with a beautifully struck 25-yard free-kick, but Jussi Jaaskelainen was equal to it.
Nonetheless, Liverpool were inspired by this initial breach of the Bolton rearguard and began to show glimpses of the confidence which overcame Everton a fortnight ago.
A dramatic goal-line clearance from Vincent Candela on 34 minutes prevented a certain tap-in for Garcia.
After the break Liverpool upped the tempo and almost had the lead when Nunez fired in a back-post volley, which Jaaskelainen struggled to gather.
A great cross from Steve Finnan was then almost diverted in by Riise from the tightest of angles, but smart work on the line from Tal Ben Haim saved the day for Bolton.
But Liverpool continued to struggle to gain any consistent attacking momentum whatsoever. They simply had no-one upfront, no-one hassling defenders and no-one chasing down.
With Morientes warming-up patiently Rafa Benitez chose lightweight Frenchman Anthony Le Tallec to come on an lead the line as the minutes ticked away and the Kop grew restless, knowing the chance to come within a point of Everton was slipping away, undoing so much of their great work in the derby triumph.
The former Real Madrid striker was overlooked again with 20 minutes to go as Vladimir Smicer entered the fray.
As the Reds boss contemplated his next attacking move, Morientes finally arrived 13 minutes from time, Bolton regained the incentive and looked the only team likely to walk away with the three points.
This was truly desperate from the home side, just three days before Italian giants Juventus visit Anfield in the biggest game to grace the stadium in a number of years.
If they perform like this the chances of the tie still being alive heading into the second leg a week later seem remote at best.
But, the Anfield faithful reckoned without the mighty Biscan who saved the day with a fine header as the crowd erupted and Liverpool continued the arduous task of clawing back the gap on Everton.
Man of the Match: Scott Carson - A series of fine saves kept the Reds in the game when his team-mates seemed determined to throw away all their hard graft in the Merseyside derby.