United were unbeaten in six as they headed to the University of Bolton Stadium, but they knew they were in for a battle with the Wanderers sat in the third automatic promotion spot ahead of kick off.
There were two changes from the weekend draw with Port Vale, with George Tanner in at right back for Danny Devine, and Josh Kayode in to replace the injured Ozzy Zanzala.
United pressed well from the kick off with Alessandra looking lively on the edge of the box. He jinked his way past two challenges, but Williams was there to close the door. Riley recycled it, and Armer was involved as he tried to make headway down the left flank. A cross spooned up off Jones but Isgrove thundered it clear.
A great flick from Patrick from an Alessandra throw brought a corner, and Guy swept it neatly towards the front stick. Kayode met it on the run, but it hit Thomason as it angled on its way to the target. That rebound came off the big forward and it dropped harmlessly wide, via the post.
There was bad news for the away side on nine minutes when Rod McDonald fell to the floor, having just completed a clearance. Nick Anderton was given the nod from the bench, and he slotted into the now vacant central defender's position.
Quick thinking from Alessandra saw him steal a loose pass midway inside the Bolton half and his touches on the run took him one-on-one with Gilks. A block on the lunge from Santos made the shot an easy one to gather for the relieved keeper.
Wanderers responded with a quick break which saw Doyle back heel a pass to the overlapping Jones. He drilled it low, across the face of goal, but there was nobody there to finish it off.
The hosts stayed forward, and Afolayan did well to make room for a cross as he went past Riley tight by the corner flag. Anderton did well to deal with the delivery.
Bolton came again and Afolayan dropped a shoulder before sending John into the box. He floated it to Doyle, who was at the back stick, and he thought he'd done everything right as he guided his header over keeper Paul Farman. Anderton had back tracked and he made a vital goal line clearance.
It was end-to-end, with Patrick showing pace at one end and Jones doing the same at the other. But it was the hosts who asked the next question when Afolayan and Lee combined to send John through. He pulled it back for Isgrove, but his effort was charged down at 18-yards.
Hayden made that block, and he did the same seconds later when Doyle took it under his wing with his back to goal. He spun, but the big defender was there to intervene.
Wanderers took the lead just before the half hour when Afolayan shrugged off a challenge tight by the touchline. He arrowed towards the penalty area and a low, fizzed shot on the run crashed back off the base of the post. The predatory Eoin Doyle was there to nudge the rebound into the waiting net, with United's appeals for offside ignored.
United had two corners on the bounce as they looked to respond, with the first spiralling over the bar as Santos got there first. Armer did the same when he met the next outswinger from Guy on the full.
Strong work from Alessandra when he was in a tight spot took him beyond John, and the quaity of his cross didn't disappoint. Kayode threw himself at it but his touch took it across the face of the nets.
A free kick from deep from Guy was kept alive by Hayden, and then Patrick, with the visitors sending plenty forward. Patrick clipped it into the mix, and Hayden cushioned it for Anderton to volley. That struck a body and went behind for a corner.
Guy pumped that one low, and it seemed to stick on the ground for an age before Isgrove smacked it away to safety. It just wouldn't settle as Kayode and Alessandra both stretched boots at it.
It was a scrappy start to the second period but United won a corner when an Alessandra throw was nodded behind. Gilks was off his line smartly to claim the resulting cross.
Left back Jack Armer was invited to go on a run by a pass from Riley and he skipped past his man before finding the six-yard box. Unfortunately Gilks was first to the ball.
There were loud appeals for a Bolton penalty when Tanner challenged Afolayan when he went on a sprint, but the officials turned away after a short period of deliberation.
A surge from Mellish had Alessandra in support as the pair tried to make something happen, but the cross from the midfielder was comfortable for the keeper.
An ambitious effort from Furman from 25-yards went high and wide as the visitors kept probing, and Bolton showed that they still had attacking intent when a training ground corner routine saw John use Lee before Brockbank was lined up for a shot. He caught it well but it ripped just over the bar.
Santos dealt with a curler from Armer that threatened to cause problems, but the defender did well to get to the loose pieces to guide it towards Kayode. There was a moment of hesitation and the chance was gone.
Armer was the supply line again when he sent a reverse pass from Patrick into the mix. Guy ducked under it, and Alessandra controlled well as he saw it late. Eight-yards out he moved into space, but his eventual shot was blocked.
The Cumbrians were even closer when another patient build up put Patrick in an advanced position. He flashed the cross low but Kayode couldn't quite get there, despite launching himself at it.
Carlisle kept going, and Mellish burst through lines to pull the ball back. Gilks gratefully put it behind with a wave of his leg. Another run of corners kept the hopes of an equaliser alive, but that spell of pressure came to an end when Armer put a header high when he came under close attention from two defenders.
Substitute Gime Toure had a speculative attempt from distance diverted by Santos, and a cross from the same man found Mellish on the move inside the box. He let fly on the turn and another corner was won. That came to nothing as Hayden headed it past the upright.
Mellish sent another Guy corner the same way, with Farman also up in attendance as the orange shirts chucked everything at it, and a Kayode long throw was cleared only as far as Alessandra. A rasper touched a Bolton man, and that was enough to take it high.
Yet another excellent Guy inswinger pinged around, but Gilks fell to the floor and the referee had to blow the whistle to allow treatment to be given.
The orange shirts had pushed and pushed, and the Bolton contingent greeted the final whistle with a loud roar, and some amount of relief that they'd seen off a real challenge.
Bolton Wanderers - Doyle (28)
Bolton Wanderers - Santos (61)
Carlisle United - Riley (56)
Bolton Wanderers - Gilks, Jones, Williams, Santos, Doyle (c), Isgrove (Elbouzedi 76), Thomason, Baptiste, John (Brockbank 59), Lee, Afolayan (Delfouneso 72). Subs - Delaney, Tutte, Miller, Gnahoua.
Carlisle United - Farman, Tanner, Hayden (c), McDonald (Anderton 9), Armer, Riley (Furman 57), Guy, Mellish, Patrick (Toure 76), Kayode, Alessandra. Subs - Norman (gk), Devine, Charters, Walker.
Referee - Martin Coy
Assistant Referee 1 - Simon Clayton
Assistant Referee 2 - Richard Wigglesworth
Fourth Official - James Adcock
Observer - Mark Brown
Attendance - BCD