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Stuart Nelson was Gillingham’s penalty hero at Colchester on Tuesday night.
The match finished level at 3-3 and in the shoot-out Nelson saved two penalties before firing home the winner himself.
Drey Wright and Sanchez Watt had twice put the hosts ahead in normal time – the second goal from a controversial penalty.
But Gills goals from Brennan Dickenson and Bradley Dack pegged them back on each occasion.
Antonio German put Gillingham 3-2 up but it was all-square again when substitute Freddie Sears struck late on to take it to penalties, which the visitors won 4-2.
Gills boss Peter Taylor made seven changes to his side for the second round Johnstone’s Paint Trophy tie.
Callum Davies captained the team, on the day he penned a contract extension, while the likes of John Egan, Doug Loft and Cody McDonald were rested.
The home side took the lead after 17 minutes with a goal from nothing. Tricky winger Sanchez Watt was dispossessed but when it ran out to Wright he spanked the ball into the top corner from 25 yards, beating Gills keeper Nelson.
Nelson was back between the sticks for the first time in a senior game since the opening match of the season - it was his 100th appearance for the club.
Gillingham were on level terms seven minutes later. Joe Martin picked out a run by Dickenson, with a long-range pass into the path of the forward and he finished well past advancing keeper Sam Walker.
The visitors were unable to build on their goal, with Nelson saving a George Moncur free-kick and Watt firing narrowly over for the hosts, after a quickly-taken corner fell kindly.
Colchester had the better of the first half but the goal that put them back ahead was controversial.
Davies was adjudged to have tripped Rhys Healey in the box and, despite no appeals from the hosts, Essex-based referee Michael Bull pointed to the spot. Sanchez converted with 39 minutes gone.
Former Gills defender Sean Clohessy dinked an effort just wide before the break.
The Gills were level again on 54 minutes when Jermaine McGlashan’s pace caught the home left-back unaware. McGlashan robbed Clohessy of possession and crossed for Dack, who applied the finish at the near-post.
Gillingham went ahead for the first time with 16 minutes left when sheer persistence from Linganzi forced the ball to German and he bundled it home from close range.
Colchester pulled it level at 3-3 with four minutes left when ex-Gills full-back Elliott Hewitt crossed for Sears to prod home past Nelson. In Colchester’s next attack Moncur put a great chance over.
In the penalty shoot-out Nelson saved from Moncur and Eastman, while Dack, Matt Fish and Hessenthaler all scored before Nelson finished the job.
Gillingham: Nelson, Fish, Martin (Hoyte 75mins), Legge, Davies, Hessenthaler, Dack, Linganzi, McGlashan, German (Millbank 75mins), Dickenson. Subs: G Morris, Hare, McKain.
Colchester: Walker, Clohessy, Eastmond, Watt, Drey Wright, Eastman, Massey (Szmondics 81mins), Moncur, Kent (David Wright 46mins), Healey (Sears 70mins), Hewitt. Subs: Lewington, Gordon.
Attendance: 1,401 (231 Gills)