The sell out game at Huish Park was played in a typical cup atmosphere with the Somerset club keen to cause an upset when coming face to face with their Premiership opponents.
Bolton manager Sam Allardyce made a number of changes to the side which drew against Arsenal at the weekend with only Kevin Nolan and El-Hadji Diouf retained in the starting eleven.
Les Ferdinand, Fernando Hierro and Tal Ben-Haim all made their first full starts for the club whilst youngster Ricky Shakes was rewarded with a full debut in the right wing back role.
The Wanderers could have gone ahead as early as the fourth minute as an inswinging corner from the left hand side by Greek international Stelios Giannakopoulos was headed towards goal by Les Ferdinand, unfortunately for the Trotters they found Yeovil's highly rated keeper Chris Weale in top form and he was able to produce an excellent low save to deny the former England striker.
Just after the quarter hour mark Bolton's Anthony Barness found himself well forward down the left hand side of the pitch and was able to find a sight at goal, however the full back was unable to keep his shot on target.
On 26 minutes Weale came to the rescue of the home side once again, saving well after finding himself in a one on one situation with Ferdinand after a good move by Bolton which involved a neat back flick by the impressive Kevin Nolan.
Nolan then almost immediately tried to catch Weale out from long range but the youngster was quick to gather a curling shot from the former England U21 international.
Eight minutes before half time the Trotters had another chance to take the lead through debutant Blessing Kaku. The on loan El-Hadji Diouf had made a good run down the left and his cross was turned into the path of Kaku by Giannakopoulos.
Just before the break the Glovers where denied an opening goal against the run of play when defender Barness made a last ditch tackle to deny centre half Terry Skiverton the chance from giving Yeovil the lead in what was a very neat passing move by the home side.
After the break El-Hadji Diouf wasted a good chance to open his Bolton account for the season screwing the ball wide of the goalmouth after Ferdinand had played a neat ball through to the Senegalese striker.
On the hour goalscoring midfielder Lee Johnson had a good long range chance to put the home side ahead with a swerving shot from 25-yards which had the Bolton goalkeeper Kevin Poole kept on his toes.
Both sides where then to make changes as the final quarter of the game dawned. Yeovil boss Gary Johnson brought on fans favourite Gavin Williams in place of Adrian Caceras and striker Kevin Gall was to replace midfielder Darren Way. Bolton introduced their current player of the year Kevin Davies in place of Les Ferdinand and were to later bring on Henrik Pedersen for Stelios.
On 72 minutes a Bolton corner was headed goalwards by Spaniard Fernando Hierro with Henrik Pedersen getting in a second header which was to thump off the Yeovil crossbar in what was a warning sign to the home team.
Soon after though, Wanderers took the lead through Brazilian defender Julio Cesar. Diouf's corner from the left was powerfully headed home by the centre half for his first goal in Bolton colours and this ultimately dejected the Glovers who had given their higher league opponents something to think about during the game.
With just five minutes to go substitute Pedersen hit the winner firing in an angled shot from the left after a good flick on by Diouf making the scoreline 2-0 to the Lancashire side.
Bolton knowing the game had been won took the opportunity to give a debut to youngster Joey O'Brien in the closing minutes. The young Ireland U19 international came on for the tiring Fernando Hierro.