Former Anfield striker David Ngog had a hand in goals for Mark Davies and Nigel Reo-Coker before Craig Bellamy reduced the deficit - only for it to be restored early in the second half by Bolton defender Gretar Steinsson.
Liverpool may have had an eye on this week's League Cup semi-final second leg with Manchester City but they struggled early on against a Bolton side which came into the game with the worst home record in English football.
After three minutes, Chris Eagles' short pass inside was helped into the path of Mark Davies by a touch from Ngog, allowing the midfielder to surge forward before placing an accurate finish past the dive of Jose Reina.
As Liverpool looked for a response, Bellamy was presented with an early shooting opportunity, thanks to the approach play of Steven Gerrard and Maxi Rodriguez, only to see his shot charged down.
However, Liverpool were left with an even stiffer challege just before the half-hour mark as Bolton broke forward with Ngog and Eagles exchanging pass before the latter lifted through the perfect through ball.
With Liverpool's defending non-existent, Reo-Coker controlled the ball well on his chest before chipping the ball neatly over the advancing Reina.
Finally, after 36 minutes, Liverpool placed themselves firmly back in contention.
Adam Bogdan's long clearance upfield was returned via the heads of Daniel Agger and Andy Carroll, permitting Bellamy to sprint clear of two defenders and convert from a dozen yards, via a touch from the Bolton keeper.
Bolton might have restored their two-goal cushion on the stroke of half-time, courtesy of Martin Petrov's curling 20-yard free-kick awarded for a foul on Ngog, but Reina did well to parry the ball.
A growing tension in the game manifested itself at the interval when a long-running feud between Bellamy and Reo-Coker ended with the pair being pulled apart on their way down the tunnel.
Nor did the tempo of on-field matters lessen after the restart, as Charlie Adam emerged from a midfield tangle with the ball and powered into the Bolton area where his shot was blocked by Steinsson.
Bolton responded swiftly, however, and a nervous Agger back pass almost played Reina into trouble and maintained the pressure on Liverpool, pressure from which the home side was able to take a grip on the game in the 50th minute.
Petrov's left-wing corner was met at the far post by Wheater with a firm header back across goal and there was Steinsson who, with no defender near him, scored his first goal of the season, with a firm and precise shot.
Bellamy, Maxi and Carroll combined in one of a number of promising Liverpool attacks but it was not until Adam whipped over a dangerous left-wing cross, forcing Bogdan into a solid piece of handling, that they could turn possession into a real threat or moment of genuine concern for the Bolton goalkeeper.
Liverpool maintained the pressure but without any real conviction. Bellamy's threatening cross was put behind by Knight, Carroll skied a half-chance over and Agger chanced his arm and saw his shot clip the cross-bar and fly onwards.
Bellamy tried to launch a late comeback by running half the length of the field and delivering a 20-yard shot which, given the ensuing deflection, Bogdan dealt with impressively.
But Bolton were just as likely to add to their tally as the game opened up and Eagles twice came close with shots from the edge of the area.
Source: AFP