Goals for strike pair Danny Kedwell and Ben Strevens, either side of half-time, gave new Gills Manager Martin Allen the perfect start to his tenure at the Priestfield helm.
With Deon Burton, Joe Martin and Jack Payne all missing from the travelling squad, Martin Allen handed debuts to four of his summer signings, namely Stuart Nelson, Tom Flanagan, Ben Strevens and Charlie Allen.
It took the visitors just two minutes to register their first effort on goal, Charlie Lee curling a free-kick just over the bar after the attacking midfielder had been brought down by Liam Fontaine, just outside the penalty area.
Gillingham, playing the neat passing style developed by Martin Allen in pre-season, looked very comfortable on the ball and bossed the opening exchanges as their Championship hosts struggled to find their rhythm.
Gerken was called into action again on 20 minutes as Matt Fish’s lofted free-kick found its way through to Danny Kedwell in the City box, but the home keeper was able to gather his header comfortably.
Bristol should have taken the lead with their first chance of the night, two minutes later, as a long ball forward was nodded into the path of Martyn Woolford, only for the Robins man to drag his low finish wide of Nelson’s left hand post.
Lee shot into the side netting from the left angle of the box, after his throw-in had been returned by Flanagan. While the home side went close at the opposite end, Pitman sending over an inviting cross from the right, Woolford arriving just too late to make a connection
With the action switching from end to end, Chris Whelpdale was denied on 28 minutes, Danny Jackman’s ball across the box cannoned off Pearson, sending Whelpdale clean through on the right but Gerkan got down smartly to save at close range.
Ten minutes later Lewis Montrose earned the first booking of the night for an overzealous challenge on Stephen Peason. It could have cost the visitors dearly as Pitman’s free-kick was cleared straight to Woolford but the lively midfielder’s shot bounced straight into the arms of Stuart Nelson.
In time added on at the end of the half Gills were awarded a penalty in somewhat bizarre circumstances. Kedwell’s powerful free-kick was blocked by Gerken, then handled on the ground by Liam Fontaine. The Bristol defender was booked, leaving Danny Kedwell to slot the resulting spot-kick into Gerkan’s bottom right corner.
The home side started the second-half at a high tempo but it was the Gills who extended their lead in the 53rd minute, Charlie Allen’s corner from the right was headed goalwards by Flanagan and forced home on the line by Ben Strevens for 2-0.
City had a chance to pull one back four minutes later as Foster and Adomah linked up well down the right flank, Skuse arrived unmarked to meet the full-back’s centre but his effort cleared Nelson’s crossbar by some distance.
The visitors almost made it three in the 62nd minute, a well-worked corner routine unpicking the home defence once more. Allen delivered to the near post this time where Whelpdale’s glancing header was well gathered by the City custodian.
Shortly after, Martin Allen shuffled his pack, handing Bradley Dack his senior debut, in place of goalscorer Strevens. While an injury to Whelpdale on 70 minutes saw Adam Birchall make his long awaited senior bow for the club.
The Robins did find the net on 78 minutes when Brett Pitman arrived at the far post to convert a deep cross from the right but his effort was cancelled out as the linesman flagged for offside. The chance marked the end of Charlie Allen’s evening as the midfielder made way for Callum Davies.
As the game entered the final stages Andy Frampton did well to check Pearson’s run and deny the City man a sight of goal before Woolford found his way into the book for barging Fish off the field as the right-back beat him for pace.
Dack and Birchall combined superbly in the closing stages, winning a series of corners to frustrate their hosts and wind down the clock. Then in the final minute of normal time the pair combined again to set up Kedwell for his second of the night only for the linesman to flag offside.
Eyebrows were raised around the ground as the fourth official conjured six minutes of additional time and sure enough the home side set nerves jangling with a goal in the fifth minute of extra time. Fish was booked for a foul on Bolasie and from the resulting kick Elliott rose above the Gills defence to head home Pitman’s free-kick.
However the goal came too late for the hosts to mount a come-back and Martin Allen’s men saw out time to record a memorable cup triumph and send the 233 travelling fans into ecstacy.
Attendance: 4,339 (233 Gillingham)
Gillingham: Stuart Nelson, Matthew Fish, Tom Flanagan, Chris Whelpdale (Adam Birchall 73), Charlie Lee, Danny Kedwell (capt), Ben Strevens (Bradley Dack 66), Danny Jackman, Andrew Frampton, Charlie Allen (Callum Davies 79), Lewis Montrose
Subs not used: Tommy Forecast, Connor Essam, Jack Evans, Charlie Webster
Bristol City: Dean Gerken, Richard Foster, Liam Fontaine (capt), Lewin Nyatanga, Jon Stead, Brett Pitman, Martyn Woolford, Cole Skuse, Stephen Pearson (Marvin Elliott 85), Jody Morris (Yannick Bolasie 64), Albert Adomah.
Subs not used: Tom Heaton, James Wilson, Paul Anderson, Joe Edwards, Joe Bryan
Referee: David Coote
Assistants: David Woolford & Christopher Powell
Fourth Official: Neil Radford