Paul Warne fired just over on 13 minutes and Lloyd Owusu brought keeper Keiren Westwood to his knees with a 27th minute header. Carlisle's best chance came just before the break when former Yeovil winger Kevin Gall brought a fine save from Romain Larrieu.
It was Gall who was to feature prominently in the 49th minute goal that gave Carlisle the lead. He got in a cross from the right and the impressive Simon Hackney was given space at the far post to finish.
Yeovil had gone 460 minutes without a league goal but they broke the spell with an excellent equaliser on 54 minutes. Anthony Barry got in a long free-kick from the left, Scott Guyett headed back at the far post and Owusu knocked in his sixth goal of the season from close range.
Within a minute, Owusu almost got another but this time Peter Murphy cleared off the line. Yeovil were now pushing for the winner and it came in the 65th minute. Kevin Betsy, who is on loan from Bristol City, was fouled 20 yards out and full-back Nathan Jones curled his free-kick into Westwood's top left-hand corner.
Yeovil boss Russell Slade was without former Premiership striker Marcus Stewart who failed a fitness test and in all had nine players missing through injury. But he said: "The lads worked hard and battled really well. We lost Lee Peltier with a recurrence of his injury and had he been there he would have taken the free-kick. As he wasn't, Nathan Jones grabbed it and it was a great goal."