United were at Fratton Park on Saturday afternoon to face the division's only unbeaten side.
And manager Paul Simpson went with an unchanged starting eleven for a fourth consecutive game as the fixture survived the worst of the bad weather, despite some heavy second half downpours.
Keeper Jokull Andresson had reported in with illness on Friday morning, so he didn't travel, with Gabe Breeze called up to the bench.
There was a half chance for Colby Bishop with just 14 seconds on the clock when a ball forward was cleared to the edge of the box. The striker volleyed but it lacked conviction and Holy completed an easy save.
Carlisle also had half a sight when a huge kick from the keeper was flicked on by Garner. Maguire scampered to cut it back, and Moxon suddenly had the angle of the box to run at. He feinted to shoot, but he was closed down and Norris accepted a hefty intervention from Rafferty.
Things remained tight, but Anjorin was lively with the ball at his feet when he found room in a packed midfied area. He bore down on goal but his shot on the run was always going wide.
The hosts worked some neat passes, with Anjorin and Kamara on the link-up, and Robertson got forward in support as they cut in from the left flank. His volley was heading for the top corner until Holy got in the way.
Kamara started and almost finished a move on 16 minutes when he once again bent inside of Back. A one-two with Morrell put him clean through, but he couldn't control it, with a heavy first touch, and Holy sprinted off his line to gather.
The big glovesman was needed again when Sparkes delivered from deep. Bishop glanced it with his forehead but Holy reacted well to pluck it out of the air.
A Moxon free kick caused problems at the other end as it skimmed off heads, but Morrell was there as cover to hook the bouncing ball clear.
Anjorin was next to swing a cross at the Carlisle front stick, with Bishop first to connect. He tried to loop the header into the roof of the net but he sent it just too high.
Maguire was scythed down by Morrell when he found a gap, 24-yards out, and Moxon fancied it. His set piece effort had power but it found the wall.
The best chance of the half for the Salads came on 24 minutes when a wicked delivery into the area was sent back across the face of the target. McCalmont was unmarked, 10-yards out, and he took a touch to set himself for the strike. It took a series of deflections and Norris was relieved when he was able to pick it up when it somehow spun into his hands.
It continued to flow from end to end and Lane beat the offside trap to latch onto a lobbed pass forward. He never seemed to be correctly balanced and he scuffed it into the deck.
Lavelle was excellent on the half hour after a misplaced pass from McCalmont had released Lane. The defender recovered to make a powerful sliding tackle just as the trigger was pulled.
Pompey thought they'd scored from their next move when Sparkes went on a sprint to meet a lovely through ball. His cross found Bishop, just five-yards out, but the in-form forward fluffed his lines with a weak connection that failed to trouble the target.
There was an almighty scramble moments later when Morrell threaded Anjorin through the defensive lines. His pull back was dangerous, and Lane got out of the way to allow Morrell to have a go. It pinged around, with Bishop going for an instinctive poke, but blocks were made and the keeper mopped things up.
Carlisle utilised a tight spot on the touchline just before the break with Fin Back at the helm. He took off down the wing and carved his way into the box. He had support, but he was stopped in his tracks by Robertson.
United were the width of the woodwork away from taking the lead just 40 seconds after the restart, after Guy had picked out McCalmont who had taken up a wonderful attacking position. He hesitated, just for a second, and that allowed Poole the time he needed to lunge in and take the sting out of a grasscutter that eventually struck the outside of the post.
A wicked near post Moxon corner was met by Lavelle, who guided it straight at the target, but it was blocked on the line. He stabbed a boot at it, and that was also going in until Norris leaned back to pull it into his chest.
Guy found a beauty of a cross when Moxon rolled a free kick from the centre circle his way, and Garner showed strength to make the header his. The nod down was too far in front of the onrushing Maguire, and he couldn't capitalise.
Armer had to step back to nod behind when Sparkes sent one long, and Holy was off his line to punch the corner away. United went on a break, but Gibson had it nicked away as he made up the yards. Moxon followed up with a long range attempt but it bent past the nets.
Holy watched a 28-yarder from Lane into his hands with the game still deadlocked, and a foul on Morrell by Garner brought a free kick opening after Saydee had cheekily poked a ball into the danger area. Lane got it on target but Holy was equal to it.
Bishop, Saydee and Kamara linked well to burst through on 68 minutes, but the home crowd were dismayed when the latter opted to cut it back rather than shoot.
Gibson, who has a habit of netting from outside the area this season, tried his luck again with ten minutes left to play after Guy had first stopped and then overturned a home attack.
The same player went for it from a similar distance after a scuffed clearance sat up his way. That one found the side netting.
There was a difficult chance for Butterworth late in the day when a Back cross was diverted his way. The deflection left him wrong-footed and he couldn't get any purchase on the header.
The substitute almost had his name in lights bang on 90 minutes when he got on the end of a superb move. Back rifled a pass to Maguire, and he set it beautifully for the thunderbolt. Butterworth was ready to celebrate, but Norris threw out a hand to claw it away from his bottom corner.
Holy was up to fingertip a Bishop header from a Sparkes centre over the bar in time added on, but there was a real sting in the tail when Shaughnessy got on the end of the resulting corner. His thumping header was unstoppable, and Fratton Park erupted as the home team claimed a victory that was extremely harsh on a visiting team who had more than played their part.
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Goals
Portsmouth - Shaughnessy (90+3)
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Bookings
Portsmouth - Rafferty (78)
Carlisle United - McCalmont (48), Guy (70), Garner (73)
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Teams
Portsmouth - Norris, Poole, Robertson (Raggett 90+4), Bishop, Morrell (c), Rafferty, Shaugnessy, Sparkes, Kamara, Anjorin (Saydee 58), Lane (Yengi 77). Subs - Schofield (gk), Ogilvie, Stevenson, Devlin.
Carlisle United - Holy, Back, Lavelle (c), Mellish, Armer, Gibson, Moxon, Guy (Robinson 84), McCalmont (Buttrerworth 69), Garner (Plange 78), Maguire. Subs - Breeze, Edmondson, Ablade, Barclay.
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Match officials
Referee - Leigh Doughty
Assistant Referee 1 - George Byrne
Assistant Referee 2 - Carl Fitch-Jackson
Fourth Official - Gary Parsons
Observer - Brett Huxtable
Coach - Gary Willard
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Attendance - 17,911 (676)