Oldham, who were beaten in their last four games, looked on course to end their dismal run with a victory before Zigor Aranalde created the chance for Holmes to make his mark.
Kevin Gall was brought down by Oldham's Richie Wellens to the left of the visitors' penalty area and Aranalde swung the free-kick across the six-yard box for Holmes to give keeper Les Pogliacomi no chance with a firm header downwards into the corner of the net.
Carlisle, with key men Karl Hawley, Paul Murray and Simon Hackney all out injured, struggled to get back into the match after Oldham took a deserved 13th minute lead.
The Latics should have gone in front after nine minutes when on-loan Leon Clarke put Paul Warne through but he hopelessly mis-hit his shot wide from 12 yards.
Playing into the wind, Carlisle couldn't seem to get out of their own half and their defence froze when Andy Liddell crossed into the six-yard box for 20-year-old Chris Taylor to arrive unmarked and score from five yards.
Taylor's celebrations of his first senior goal in 51 Oldham appearances earned him a booking.
Carlisle struggled to pull level with Gall hitting the bar from a wide angle and Pogliacomi diving to hold an Aranalde drive at the foot of his post.
Danny Graham headed straight at the Oldham keeper a minute before half-time but, clearly struggling to shrug off a knock, made way for Holmes ten minutes into the second half.
Soon after coming on the big striker got on the end of a long throw from man of the match Aranalde but screwed his 15 yard shot wide.
And Aranalde got in a vital block when Liddell ghosted in on a far post cross that was allowed to bounce across the Carlisle six-yard box.
Pogliacomi denied Gall an equaliser with a fine 69th minute save when he turned the Carlisle man's header around the post after Aranalde's pinpoint cross.
But the Spaniard wouldn't be denied and set up Carlisle's goal with an equally accurate free-kick.