Carlisle United were once again left to wonder how they had nothing to show from a game they dominated for long spells without quite managing to completely turn the screw.
The Cumbrians almost drew first blood with just 37 seconds on the clock when Chimbonda clipped a lovely pass into the area. Miller shrugged his marker off, and went one-on-one with the keeper, but he was disappointed to see his powerful drive ricochet away off the base of the upright.
More good work down the right flank from Chimbonda and Amoo found the visitors light at the back. Miller once again showed for the ball but his neat chip into the back of the net was ruled out for offside.
The Gills settled and a free kick from deep caused all kinds of problems as it whipped into the box. McDonald rose to meet it and his thundering header went close as it flew just past the target.
Courtney Meppen-Walter stood strong to make a vital block when Gregory crunched an accurate shot from distance, and Berrett pulled away in frustration at the other end when he tried the same as the ball bounced up at his feet.
Flowing and incisive football from the home side created a fantastic chance for the in-form Brad Potts when Miller nodded a dipping pass into his path on the edge of the box. The big midfielder struck the volley cleanly on the run but Nelson dived to make the save and beat the ball away.
Carlisle kept the pressure on and an early cross from Robson had Miller making a move in front of the keeper. Leon Legge intervened to nod the cross over his own bar.
United were in control and Meppen-Walter caused panic when he volleyed a deep free kick back into the box. It caught the Gills' back line by surprise and Legge was relieved to be able to hook it away as it pinged around dangerously.
Robson saw plenty of the ball and another low delivery brought Miller to the near post. He touched it and pulled it back but it was behind Drennan and Gillingham were once again able to sweep it away.
Gillingham reminded their hosts that they could cause threats of their own when hesitancy from Meppen-Walter brought them a corner from nothing. Carlisle struggled to clear and Pickford was needed to tip a stinging Barrett volley over the bar as he searched for the roof of the net.
The second delivery caught in the wind but it was kept alive and Pickford showed quality again as he held his position. Leon Legge spun and shot through bodies but the keeper stood tall and pushed the shot away to safety.
Possession drifted back in favour of Carlisle and an Amoo run sparked a string of difficult corners. James Berrett found himself with half a sight of the nets but he couldn't keep his volley down and it flew high into the stands.
Matt Robson was next to go close when he wrapped his boot round a bouncing ball 35 yards out. The technique was excellent but Nelson was happy enough to watch it go over.
Gillingham used the conditions well for their set pieces and Dack sent another one deep as he picked out Harriman with a lovely pass. O'Hanlon watched the header closely and was able to tidy things up as McDonald waited to connect.
A switch to the left flank for Amoo brought another increase in tempo for the Cumbrians but the Gills kept it tight as they mopped up the second ball.
Carlisle comfortably bossed the possession in the middle of the park but they were undone just before half time when Gillingham broke as an Ekangamene volley was blocked on the edge of their own area. McDonald called for it and the tackle from Chimbonda, which stopped him in his tracks as he cut inside, set the ball up nicely for Joe Pigott. He took two touches before he picked his spot in the bottom corner.
A frustrating first half was summed up in time added on when a lovely touch from Miller left Villa loanee Michael Drennan with a chance to wind one up from distance. Nelson was beaten but it pinged back off the inside of the post and Potts could only stab his follow up wide as it bounced awkwardly in front of him.
The second half took a while to get going in awful conditions and a Nelson spill from an Amoo shot brought brief excitement as the driving wind and rain won the day.
Gillingham fashioned the first real opening of the half when Fagan was played into the box by a neat pass from McDonald. The shot was on target but Pickford was well placed to deal with it.
Miller and Potts sent long range shots over the bar in response, but Carlisle survived a real scare when McDonald took a ball over the top on his chest. His second touch took him past Pickford but the referee waved play on as the striker fell to the floor.
United broke from deep as they cleared the loose ball and Amoo had his head in his hands as he crashed a goal-bound shot into Drennan. The ball eventually ran for a corner and Carlisle celebrations were cut short when Miller's header beat Nelson only to bounce back off the inside of the post.
Danny Redmond came on to make his debut with 20 minutes left to play and his first contribution was an inswinging free kick which just edged its way past the post.
A long kick forward from Pickford brought a nice flick from Drennan and Miller suddenly found himself through with just the keeper to beat. The big striker went for an early volley and Nelson grabbed it as it came at his chest.
Potts was then sent into the area but he lost his balance as he shot at pace and it rose high into the sky and over the goal.
United kept the pressure on but Gillingham made it comfortable when Meppen-Walter misjudged another high ball over the top. His touch set McDonald through on goal and he made no mistake as he clipped it over the advancing stopper.
A Legge own goal made things interesting with 60 seconds left to play and a string of Carlisle corners brought hope as the Gills struggled to clear. And substitute Sam Byrne wheeled away in disappointment right at the death when his header from a Chimbonda cross bent straight into Nelson's midriff.
United - Legge (og 90)
Gills - Pigott (43), McDonald (88)
United - Chimbonda (37), Redmond (77)
Carlisle United - Pickford, Chimbonda, O'Hanlon, Meppen-Walter, Robson, Potts, Ekangamene (Redmond 70), Berrett, Amoo, Miller, Drennan (Byrne 83). Subs - Fleming, Noble, Thirlwell, Symington, Guy.
Gillingham - Nelson, Martin, Linganzi, Legge, McDonald, Gregory, Dack, Smith (Fagan 21), Harriman, Barrett, Pigott (Akinfenwa 64). Subs - Baxter, Davies, Lee, Hare, Hessenthaler.
Referee - Mr Mark Heywood
Attendance - 3,584 (194 away fans)