Mark Gillespie, Paddy Madden and Frank Simek came into the starting line up for the visit of local rivals Preston in the Johnstone's Paint Trophy first round with manager Greg Abbott looking for a response following the disappointing trip to MK Dons at the weekend.
But United missed out on penalty kicks when three consecutive misses allowed David Buchanan to send his side through with a well placed strike in the top corner.
"A penalty shoot-out is a 50:50 situation and you go through almost on the spin of a coin,"manager Greg Abbott said.
"We've had our fair share of wins with them and it's just disappointing for the effort the players have put in. They competed very well and created numerous chances against difficult opposition, particularly with the way they approach their football matches."
Carlisle got forward early with a ball over the top from McGovern which found Berrett in space. He clipped an early cross into the area but Robertson crept across to hook it clear.
And the visitors sent shock waves round Brunton Park when they took the lead with their first attack of the night with just four minutes on the clock. Amoo stole a yard at the back post and set himself to volley the ball as it landed at his feet. He lost his balance, but his effort somehow found Beardsley who was able to guide it in past the stranded United keeper.
Peter Murphy had to head clear from a Hayhurst cross as Preston stayed forward, but United should have been back on level terms when McGovern sent Jervis one-on-one with the keeper. The ball sat up nicely but the big striker was disappointed to see his attempted lob sail over the bar.
United started to take a grip on the game and Edwards had a volley blocked as McGovern delivered a string of dangerous corners into the area. Peter Murphy then swiped a long range volley just over the target as it looked increasingly likely that the Cumbrians would find a way through.
Madden stayed alert as Preston struggled to clear their lines and he was a ball's width away from converting a weak back pass until Simonsen arrived on the scene to save the day.
Matt Robson looked dangerous on the half hour and bravery from Keane prevented a sweetly struck volley from testing the target.
The visitors reminded Carlisle that there was defending to do just before the break when Amoo turned away from Murphy and headed for the edge of the box. Beardsley was on the end of the cross but his celebrations were cut short by an offside flag.
A neat pass Noble at the other end brought Simonsen off his line and he had to punch firmly as Madden tried to make it his own. And the Irish-under 21 striker was the man on the spot again as he whisked a volley from a Jervis nod down into the terracing behind the goal.
The Cumbrians started the second half in determined mood and a run from Robson took him to the bye line. His cross looked inviting but it curled agonisingly behind the onrushing blue shirts.
And Robson brought the save of the night out of Simonsen when he rose to greet a Noble cross at the far post. His header had direction and power but the keeper somehow stopped it before it crossed the line.
The United left was suddenly the main threat and he put another volley over when he arrived late following good work from Chantler and Berrett. His next effort came after a run down the left flank which needed a diving save at the near post as it threatened to edge in.
Frank Simek received orders from the bench to push forward and his unexpected cross brought a slip from a wrong-footed defender. Jervis was in position but he took his eye off the ball and failed to connect as the ball bounced away.
The good work from Carlisle finally paid off when McGovern bided his time with the ball dropping from high. He arched his body and rasped a wonderful volley into the bottom corner.
Preston sat deep as they tried to contain their hosts but they were given a boost when Liam Noble was shown a red card for an aggressive challenge in the middle of the park.
Substitute Akpo Sodje should have done better when he headed over from close range with the clock ticking down and the same player rattled the woodwork when he should have done better when the visitors carved their way down the left flank.
But it was United who could have nicked it right at the death when a Jervis flick rebounded off teenager Brad Potts. Simonsen was beaten but the ball shaved the angle of post and bar on its way into the Warwick.
"When it came to the penalties Tony Caig just told me it was my chance to be a hero," Mark Gillespie said. "He talked about a few of the shoot-outs he'd been involved with and gave me a few tips on how to treat it all.
"I've never been involved in one before, not even at youth level, so it was a new experience. I'm glad I saved one but I'm gutted that we lost the game that way.
"When I got to that one I did allow myself to think that it was going to be my night after all. Anything can happen with penalties though and, like I say, it's just disappointing that we didn't go through."
United - McGovern (68)
Preston - Beardsley (4)
Jervis MISS: 1-1
Wright MISS: 1-1
Berrett MISS: 1-1
Madden MISS: 1-2
Preston go through 3-1 on penalties
United - Berrett (54), Noble (sent off 83, straight red card)
Preston - Amoo (16), Keane (49), Sodje (88)
Carlisle United - Gillespie, Simek, Edwards, Murphy, Chantler, McGovern, Berrett, Noble, Robson (Potts 90), Madden, Jervis. Subs - Collin, Beck, Symington, O'Halloran.
Preston North End - Simonsen, Keane, Robertson, Amoo, Cummins (Wroe 53), Buchanan, Procter, Beardsley (Sodje 79), King, Hayhurst (Monakana 64), Wright. Subs - Stuckmann, Laird.
Ref: Mr Jeremy Simpson
Attendance: 3,471(376 away fans)