Richard Logan's double and a tap in for Ryan Harley helped City to eighth in League One and means the Grecians have matched last season's tally of away wins.
On a day where both sides remembered Adam Stansfield his former strike partner made the decisive breakthrough on 23 minutes, firing in from close range after a classy flick from Richard Duffy.
The home side drew level when Sam Williams sent a looping header into the top corner but just seconds later Logan slotted home after Bertie Cozic's surging run through the Yeovil defence.
Harley set up a comfortable finale when he converted Jamie Cureton's right-footed cross.
With games coming thick and fast Paul Tisdale decided to freshen up his midfield with the impressive Cozic starting for the first time this season along with David Noble. The pair replaced Liam Sercombe and James Dunne showing just how many options the City boss has at his disposal.
Daniel Nardiello was initially named as a substitute but Joe Heath took his place after Tisdale decided not to risk the Welsh striker, who was feeling stiff, with another game just three days away.
The opening exchanges this afternoon was worlds away from the frantic finale we saw on Tuesday night with no real chances of note during the opening 17 minutes. Harley was initially dispatched behind Cozic and Noble but swapped places with City's number eight as the game passed the 15 minute mark.
Troy Archibald-Henville was the star man on Tuesday and it his interception that stopped Dean Bowditch opening the scoring two minutes later. The striker found himself in acres of space, rounded Paul Jones, and his goalbound shot was blocked by the long legs of the former Spurs centre-back.
Owain Tudor Jones shot wide and at the other end a Billy Jones free kick was straight into on loan keeper Stephen Henderson's hands.
His digits were picking the ball out of the back of the net shortly after when Logan put the finishing touches to a really high-quality move. Cozic did superbly well in midfield to win the ball with a thundering challenge. Logan picked up the Frenchman's pass and fed Noble on the edge of the box. He sent the ball out wide to Scott Golbourne whose left-footed cross was flicked on at the near post by Duffy and converted at the back post by a delighted Logie.
The players celebrated what was a very enjoyable goal with the 1,900 travelling supporters behind the goal, Jamie Cureton and Logan in particular were clearly enjoying the opening goal.
Left-back Nathan Smith had the next real chance of the match, weaving through a sea of red and white shirts before shooting over.
His team-mate Bowditch then had the ball in the back of the net with a low drive but was flagged for offside. At the other end the away fans were left fuming by referee Iain Williamson's decision to award Yeovil a free-kick after Steve Tully was seemingly pulled down by Andrew Welsh right on the edge of the box.
Paul Jones' crossbar was then left shaking minutes later after a thunderbolt of an effort from Gavin Williams cracked off the woodwork.
Cureton then missed a great chance to give City that vital second. Cozic fed Harley who slipped Cureton through on the right-hand side of goal but he lifted his effort over the bar. In first half stoppage time Williams sent a dangerous free-kick goalbound which was headed up and over the bar by the backpeddling Duffy.
The first real chances of the second period fell to Andrew Williams who twice headed wide of Paul Jones' goal but then his name-sake Sam, who had only been on the pitch for two minutes drew Yeovil level.
Gavin Williams sent an inch perfect cross into the box and up rose Sam Williams to send a looping header into the back of the net with his first touch.
In the Johnstone's Paint Trophy clash here just weeks ago Yeovil conceded a minute after equalising, and lightning struck twice here with Logan scoring his fourth of the season just seconds later.
Cozic set off on one of his trademark 'barrel-chested' runs forward before slipping the ball through to City's number 20 who had the simple task of sending a low shot into the corner to put the Grecians back in the lead.
Logan's celebrations saw him point to the sky in tribute to Stansfield whose three children were the matchday mascots at today's match.
Noble and Harley both picked up yellow cards before Tisdale decided to shuffle his pack with Dunne and Sercombe being introduced for Noble and Cozic. With a new-look midfield in place City continued to press forward in search of the vital third and they got it on 75 minutes.
Cureton got to the touchline and sent a high cross to the backpost and there was Harley to add to his increasingly impressive goal-tally for the season.
The pair combined again shortly after, Harley's corner finding the former Norwich man at the far post but his volley was deflected wide. The striker, who scored twice here in the JPT, then hit the post with a low effort and when the ball bounced out into the box Harley's half-volley was well saved by Henderson.
City then comfortably played out the final ten minutes or so with neither team really threatening. A tough trip to Bournemouth awaits on Tuesday but if City can replicate this performance then the unbeaten run could be extended to six games on the South Coast.