Liverpool were unable to extend their winning run to 11 games, failing to equal a club record set in 1982.
Radhi Jaidi had given Bolton a 10th minute lead, heading in to capitalise on goalkeeper Jose Reina's blunder.
Liverpool pulled level midway through the second half when Steven Gerrard won and expertly converted a penalty.
Four minutes later El Hadji Diouf bundled in Kevin Davies' cross, but Luis Garcia's chest control gave him the space to volley in the equaliser.
Liverpool's 10-match winning streak has had much to do with Reina's confident goalkeeping.
He has conceded just one goal during that run, but his assuredness evaporated in an instant as Stylianos Giannakopoulos's free-kick hung in the air.
The Spanish keeper dropped the cross and then in a mix-up with Sami Hyypia, the ball richocheted to Jaidi, who nodded home.
Just past the half-hour Jaidi almost snatched a second goal when he collected a cross from Giannakopoulos and unleashed a powerful shot that was well blocked by Steve Finnan.
Kevin Nolan's jinking run then had Liverpool at sixes and seven until Jamie Carragher got in a saving tackle, though the Bolton midfielder claimed he should have had a penalty after the England defender made a second less well timed intervention.
Bolton's aggressive approach increasingly began to rile Liverpool and in the space of a couple of minutes both Peter Crouch and Carragher were booked.
Liverpool took their time to establish any sort of attacking rhythm in that first-half but they went close with a trio of shots.
First Ricardo Gardner blocked a Gerrard volley and then Jussi Jaaskelainen dived low to push away Dietmar Hamann's skimming shot.
And just before the interval Bolton's goalkeeper did just as well in beating away a fierce Djimi Traore shot.
During the first half Liverpool were clearly unsettled by Bolton's aggressive approach.
At times the game threatened to boil over with Mohamed Sissoko guilty of an ugly challenge on Diouf that was missed by referee Mark Clattenburg.
Nolan was also furious with Gerrard after the Liverpool captain's boot came down heavily on the Bolton's midfielder's chest while he was lying on the ground.
In a bid to rescue the game Liverpool manager Rafael Benitez introduced Spanish duo Xabi Alonso and Garcia.
Soon after that switch Liverpool drew level when Gerrard enticed O'Brien into a rash challenge.
The Liverpool captain gave Jaaskelainen no chance with a penalty that was expertly despatched into the corner of the net.
Having worked so hard for the equaliser Liverpool soon found themselves chasing the game again.
Kevin Davies cross from the left found Liverpool oldboy Diouf, who scrambled the ball home as Reina dithered.
But with eight minutes to go Alonso and Garcia combined to provide Liverpool with a second equaliser.
Alonso picked out Garcia, who chested the ball down, before rifling a shot into the corner.
Bolton manager Sam Allardyce:
"People talk about us being tough but Gerrard stamped on Nolan and Mohamed Sissoko also stamped on El Hadji Diouf.
"Gerrard looks at Kevin before he does it and in a game of football that needs to be punished.
"The referre hasn't seen it - we don't want the FA seeing it afterwards."
Liverpool manager Rafael Benitez:
"We deserved to win - we have done a lot of things for winning.
"I was surprised at some of the decisions in the game and to see players diving. It's a different idea of the rules that I have.
"There was a foul against Peter Crouch before Bolton's second goal, but I don't want to talk about the referee."
Bolton: Jaaskelainen, O'Brien, Jaidi, N'Gotty, Gardner, Faye, Nolan, Giannakopoulos, Speed (Fadiga 90), Diouf (Ben Haim 83), Davies.
Subs Not Used: Borgetti, Vaz Te, Walker.
Booked: Faye, Nolan.
Goals: Jaidi 10, Diouf 71.
Liverpool: Reina, Finnan, Carragher, Hyypia, Traore, Gerrard, Hamann (Alonso 64), Sissoko (Cisse 83), Kewell, Sinama Pongolle (Luis Garcia 62), Crouch.
Subs Not Used: Riise, Carson.
Booked: Crouch, Carragher, Sissoko.
Goals: Gerrard 67 pen, Luis Garcia 82.
Ref: M Clattenburg (Co Durham).