With the game at 1-0, Ged Brannan's spot-kick was well saved by Keiren Westwood and the Cumbrians didn't look back.
Holmes' sixth minute strike was meant as a cross for Karl Hawley, but the ball instead dipped over Paul Crichton and in off the far post for his first goal since his move from Bournemouth.
Taking an early lead, Carlisle kept Stanley at arms length and except for the penalty, Westwood had very little to do.
The points were wrapped for the home side early in the second half after good work from substitute Magno Vieira.
The Brazilian's neat flick found Hawley clean through and from the left corner of the penalty area he fired past Crichton to kill off Stanley.
Now two goals down the away side pushed forward, but with little creativity they rarely troubled Westwood and will be thankful to get out of Cumbria with a 2-0 defeat.