United went into the second of their Central League Cup group fixtures in second place in the table having seen off Morecambe in the first of their encounters.
Championship side Wigan Athletic were the visitors and they fielded their under-23 sid as they looked to climb up the table.
It was a tight start to the game, with both sides struggling to create, but Olomola did well when he had his back to goal. He spun to shoot but Long made the block.
The visitors had a good spell but O'Neil was wasteful on two occasions when he had the ball inside the box. His first shot, from just 10-yards after Crankshaw had cut the ball back, was on the rise and going high from the moment it left his boot.
His second volley was wild as he screwed it well wide, again from short range.
It became a real midfield tussle but Wigan thought they'd done enough on the half hour when a long kick from Jones was picked up by Golden. His back post cross came to Baningime, and a stinging volley brought a superb save from Gray as he spread himself to stop the shot.
Gray was needed again moments later when O'Neil was sent clean through. A rasping drive was heading for the top corner until the stopper went full length to tip it over.
There was an almighty goalmouth scramble just before the break when Webber nodded a cross back across the face of goal. The ball pinged around, and Sanders missed a real chance as it fell onto his boot. All he had to do was find the net, but he lost his balance and a poor toe poke went wide.
United fashioned the first real chance of the second half when Sorensen and Olomola combined to bring Elliott into the equation. He shot from distance but it whipped just over the bar.
Wigan had another scramble inside the six-yard box when Jolley won a header from a corner, but it wouldn't fall kindly and Crankshaw was flagged offside just as he shaped to pull the trigger as Golden sent it his way.
O'Neil blazed one over the bar as the game remained locked in a stalemate, and Golden did the same when he was sent clear in the next attack.
There was more danger from the lively O'Neil as he bent a run past two challenges to get into the box. His shot was angled for the bottom corner but it swerved late and shaved the woodwork.
In a second half of very few clear-cut chances Sanders wasted a good opening when a free kick delivery eventually came back his way. It was a powerful attempt but never really under control.
Wigan scored the all-important goal with a minute left to play when a high ball was nodded into the area. Charlie Jolley jumped highest and he left Gray with no chance as he looped what looked to be the winner into the back of the net.
But United had the last say when Major whisked a great ball into the area. Charlie Barnes was onto it and he smashed a cool volley past Jones and into the waiting target.
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Goals
Carlisle United - Barnes (90)
Wigan Athletic - C Jolley (89)
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Bookings
Carlisle United - Birch (21), Kerr (84)
Wigan Athletic - Smith (25), O'Neil (32)
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Teams
Carlisle United - Gray (c), Barnes, Birch, Sagaf, Wilson, Lightfoot, Elliott, Sorensen (Soper 70), Armstrong (Major 57), Olomola (Kerr 57), Charters.
Wigan Athletic - Jones (gk), Golden, Webber (Galvin 70), Sanders, Long, Smith (c), O'Neil (Aasgaard 82), Weir, C Jolley, Crankshaw, Baningime. Subs - H Jolley, Obi, Perry.
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Referee - Darren Williams