Bolton progressed into the third round of the Carling Cup thanks to a strike from Mark Davies just before half-time.
The midfielder notched his first goal for the club with a well taken finish from ten yards out after combining well with Kevin Davies on 41 minutes.
The victory was a thoroughly professional performance from a full-strength Bolton side who were in no danger of exiting the competition at any stage of the evening.
Indeed, the scoreline could have been much more favourable for the Trotters in a game they fully dominated.
The hardworking Johan Elmander was unfortunate not to get his goalscoring tally up and running for the season as he was denied by some fabulous goalkeeping by Luke Daniels late in the second half.
Jlloyd Samuel was drafted back into the starting line-up by boss Gary Megson in the only change from the weekend's defeat at Hull City.
It was from the recalled full-back's cross that Wanderers carved out their first penetrating attack of the evening as a low delivery was deflected right through Tranmere's six-yard box and just out of the reach of Johan Elmander with just five minutes played.
Former Liverpool midfielder John Welsh had a shot from 25-yards comfortably claimed by Jussi Jaaskelainen in a typical brisk-paced opening to the cup tie. The home supporters, aided by a thudding drum beat, were in good voice with the 1,000 strong contingent of travelling Wanderers fans also vocally encouraging their side.
With 18 minutes on the clock, Alan Mahon twice caused concern for Wanderers rearguard with two devilish left-footed crosses, but on both occasions the defensive unit held strong and comfortably cleared any potential danger.
The pace simmered as the half progressed as both team seemed content to try and keep possession and create opportunities through a patient approach. It was from a steady build-up that Elmander had his first sight on goal, but in finding space inside the penalty area, he drifted the wrong side of Ian Goodison and was subsequently denied by both goalkeeper Luke Daniels and the linesman's flag.
Matt Taylor almost opened his season's account with a headed attempt on the half hour mark. Sam Ricketts turned Aaron Cresswell inside and out before whipping across an inch perfect cross that Taylor put fractionally over the crossbar following a well-timed leap.
That chance was the highlight of what was largely a quiet first half up until the opening goal of the game on 41 minutes.
It was Mark Davies who started and finished a clinical Wanderers break, as after picking the ball up in midfield, he jinked through the centre of the park before releasing captain Kevin Davies. The former Wolves midfielder continued his run forward, seizing on a precise slide-rule pass from his namesake before firing low past the left hand of Tranmere stopper Daniels to give his side a half-time lead.
With Wanderers now having a stranglehold on the contest, they continued to boss proceedings well into the second half. Fabrice Muamba had a goal-bound shot charged down, Sean Davis saw a deflected attempt land on the roof of the net and Kevin Davies was within a whisker of latching onto a Mark Davies cross all within 15 minutes of the restart.
The 65th minute saw the introduction of three substitutes, two from the home side and one from Gary Megson. Mark Davies received a standing ovation from the Bolton supporters when he was replaced by Lee Chung-Yong, but the reception for Michael Ricketts couldn't have been more opposite, who was making just his second appearance for his latest club.
The introduction of Chung-Yong gave Wanderers an added impetus down the right wing with his nimble football and obvious skill left full-back Cresswell bamboozled on a couple of occasions.
Johan Elmander had suffered plenty of tough luck in front of goal in 2009 and he could scarcely believe that he hadn't opened his account for the season with just 14 minutes remaining. Matt Taylor's precise header across goal landed perfectly for Elmander, who nodded goalwards from just four yards out. There was little wrong with the finish, just a brilliant point-blank save from Daniels.
McCann was brought on by Megson as the game approached its latter stages and the midfielder offered a calming presence when he replaced the impressive Muamba. Elmander came close again with a ferocious long-range effort that was tipped fantastically around the post and Matt Taylor blazed wide&nbsp; from just inside the penalty area as Wanderers pressed for the killer second goal.
There was a late scare when substitute Fraughan found space inside the area in stoppage time, but he could not force the match into extra-time with a shot that hit the wrong side of the netting.
Tranmere: Daniels, Cresswell, Edds, Goodison, McLaren, Mahon (Fraughan 78), Welsh, Taylor, Gornell, Shuker (Barnett 65), Curran (Ricketts 65) (Subs not used: Broomes, Collister, MacAuley, Fraughan)
Bolton: Jaaskelainen, Cahill, Knight, Samuel, Ricketts, Mark Davies (Chung-Yong 65), Davis, Muamba (McCann 79), Taylor, Elmander, Kevin Davies (Subs not used: Al Habsi, Steinsson, Robinson, O'Brien, Ward)