Sam Allardyce's team went ahead with a disputed goal after Jose Reina was wrongfully penalised for handball.
Playing his 750th league game, Gary Speed inflicted maximum punishment on Liverpool as he arrowed in a free-kick.
Bolton extended their lead when Ivan Campo thumped a header against the bar and over the line from Kevin Davies' cross early in the second half.
Both goalscorers typified that grit as they both made important defensive interventions as Liverpool threatened.
In the first half, Speed got back to tackle Jermaine Pennant, while after Campo had scored his goal, the former Real Madrid player was soon stretching to stop Jamie Carragher's pass reaching Luis Garcia.
Abdoulaye Faye was booked for a crude tackle on Steven Gerrard, while Dirk Kuyt was left with a bloody head after he was involved in a clash of heads with the Bolton defender.
Liverpool's pain was further increased when they fell behind in controversial circumstances. Reina was penalised for handling outside of his area, though television replays showed the Spaniard released the ball when he was clearly inside in his box. Reina was made to pay for linesman Andy Halliday's mistake as Speed's low left-footed shot flew into the corner of the net.
The former Villareal goalkeeper has had an uncertain start to this season and in trying to save Speed's free-kick he made the strange decision to dive in the space his wall was protecting as the ball went the other way.
Speed's strike was Bolton's only direct shot at goal in the first half.
Either side of Speed's goal, Liverpool had chances to score.
Alonso's sweetly-struck volley hit the base of the post, while Jussi Jaaskelainen reacted quickly to beat away Gerrard's powerful shot.
On 51 minutes Davies delivered a cross from the right that was met by Campo with a thumping header that rebounded off the bar and over the line with Reina well beaten.
Interview: Liverpool boss Rafa Benitez
Interview: Bolton first-team coach Ricky Sbragia