Veteran striker Steve Guinan put the visitors ahead on seven minutes when he hammered home from the edge of the box. Carlisle then had a 20-minute spell when they could have easily gone in front but Graham Kavanagh, Lewis Neal and Danny Graham all failed to hit the net.
Those misses proved costly as Hereford doubled their lead on 24 minutes. Carlisle failed to clear the ball and when Fabian Brandy, on loan from Manchester United, fed Guinan he crossed to Ben Smith to poke home the second.
Michael Bridges then missed a sitter from twelve yards but he made amends on the stroke of half time, firing into the top corner from 30 yards. It was the same story in the second half. Carlisle dominated proceedings but could not find that killer instinct. Kavanagh hit the post just after the re-start when Bridges slid him in.
Neal's in-swinging corner was cleared off the line and Graham, Kavanagh and Joe Anyinsah all had good chances. With just ten minutes remaining, substitute Scott Dobie had a fantastic chance to equalise but somehow missed his header from inside the six-yard box.
Carlisle keeper Ben Williams saved well from Brandy but a chorus of boos was left ringing in the ears of Carlisle boss Greg Abbott as the final whistle sounded. The home side left just three points above Yeovil having played two games more than the West Country club.