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Last season’s star man Connor Ogilvie was Gillingham’s matchwinner in Saturday’s Carabao Cup first round match.
The Gills played over half an hour with 10 men after Ryan Jackson’s competitive Priestfield return ended with a red card, after picking up two bookings.
Southend struck the woodwork twice in the second half but the home side hung on for a place in round two.
Summer signings Ryan Jackson, Christian Maghoma, Zech Medley, Kyle Dempsey - named as captain - Robbie McKenzie, Vadaine Oliver and Alex MacDonald all started.
The Gills took some time to grow into the game, six months after their last competitive fixture, with Southend wide-man Jordan Green causing problems down the left flank.
Green almost teed up Isaac Hutchinson but the Southend man twice had shots blocked and McKenzie managed to clear.
McKenzie was playing as part of a three-man Gills defence, Ogilvie and Jackson playing the wing-back roles from the off.
Home keeper Jack Bonham needed to be alert to hold onto Elvis Bwomono’s long-range effort.
Ogilvie headed in the winner when the teams met in League 1 at Roots Hall back in February and he was there again to put the Gills infront against Southend, running onto Dempsey’s cross and heading in across the keeper Mark Oxley.
Charlie Kelman flashed a shot wide for Southend but as the half progressed more chances went Gills’ way, Akinde making his presence felt, but unable to divert any of his first half headers on target.
Just before the break Akinde showed his strength to turn defender John White but the Southend man recovered well to block the resulting shot.
Vadaine Oliver headed a great chance wide early in the second half, having time and space from a Jackson cross. At the other end another routine stop from Bonham denied Hutchinson.
The Gills were down to 10 men on 57 minutes after Jackson picked up a second caution. Already on a booking after a clash with Hutchinson just before the break, he received another yellow as Green went down out wide as Southend looked to break.
Gills were left unhappy when card-happy ref Christopher Pollard kept them in his pocket after Southend defender White - who had already been booked - escaped punishment after leaving Stuart O’Keefe in a heap.
Blocks were made to deny Southend’s Kelman and Hutchinson as the visitors looked to get back into the tie. Midfielder Hutchinson went closer still with a free-kick from 25 yards that bounced clear off Bonham’s near post.
The Gills keeper made a great low save in the final minute to deny Lewis Gard, the Southend man drilling an effort at goal after it opened up for him. Stephen Humphry also smashed a shot wide and Kelman thumped an effort against the post.
Gillingham: Bonham, Jackson, Ogilvie, O’Keefe, Maghoma (Tucker 63mins), Medley, Dempsey, McKenzie, Akinde, MacDonald (Willock 75mins), Oliver (Coyle 68mins). Subs not used: Walsh, Mellis, Woods.
Southend: Oxley, Bwomono, White, Hobson, Taylor (Humphrys 70mins), Green, Hutchinson, Dieng (Gard 63mins), Egbri (Kinali 88mins), Kelman, Goodship. Subs not used: Seaden, Phillips, Mitchell-Nelson.