Julio Cesar and Henrik Pederson were on target as last season's Carling Cup runners-up reached the third round.
Chris Weale saved well to deny Les Ferdinand after Ricky Shakes and Kevin Nolan set him up, before Weale produced another fine stop from Blessing Kaku.
El-Hadji Diouf shot wide after racing clear, while Lee Johnson and Andrejs went close for the home side.
Pedersen headed against the bar before Cesar headed in Diouf's cross and the Dane's firm drive sealed victory.
Yeovil: Weale, O'Brien, Skiverton, Fontaine, Rose, Terry, Way (Gall 64), Johnson, Caceres (Gavin Williams 63), Jevons, Stolcers (Tarachulski 81).
Subs Not Used: Miles, Collis.
Bolton: Poole, Ben Haim, Barness, Cesar, Shakes, Nolan, Hierro (O'Brien 88), Kaku, Diouf, Giannakopoulos (Pedersen 70), Ferdinand (Davies 64).
Subs Not Used: Oakes, Talbot.
Goals: Cesar 80, Pedersen 87.
Ref: D Gallagher (Oxfordshire).