Gillingham had a ‘goal’ controversially ruled out as they were beaten in the Checkatrade Trophy on Tuesday night.

Alex Mowatt won it with an injury-time strike but the Gills will feel hard done by.

With the score tied at 1-1, Josh Parker was denied, replays showing his shot going over the line, after a stunning effort that had rattled the woodwork.

Mark Byrne had put the Gills ahead from the penalty spot early in the game but several other great chances were missed before Oxford levelled through Jack Payne.

Gillingham won all three of their group games, ending their round one qualifying game with a memorable 7-5 win over Reading.

Both teams fielded strong teams for the match, Gillingham bringing back captain Lee Martin into their XI and Oxford starting their main man Payne.

Gills’ main changes came in defence, handing Alex Lacey his first start since the home game with Scunthorpe at the end of September. Ben Nugent was making his first start in two months.

Oxford – losing Trophy finalists for the previous two seasons – had benefitted from a training camp in Spain prior to the match but looked rusty at the back.

Their sloppiness created a number of chances for the Gills who had their tails up in the early stages. It was Scott Wagstaff’s quick interchange with Parker that led to the early penalty, which Byrne dispatched in the ninth minute.

Moments later Conor Wilkinson was gifted the chance of a second, after more sloppy play at the back, but a heavy touch led to keeper Simon Eastwood claiming the ball.

Prior to those chances Parker had bamboozled visiting skipper John Mousinho – a former Gills loanee – before firing wide.

Parker had another good chance blocked but as the half wore on Oxford settled and the gifts stopped coming.

Jon Obika same close to converting Josh Ruffels’ dangerous cross and Obika soo after played in James Henry, who forced a save from Stuart Nelson.

The equaliser came in the 31 minute and it was Payne with a smart finish, finding the far corner with a shot across Nelson. Gillingham had failed to clear the ball in the build-up, which had seen Byrne clearing off the line from Obika.

Gillingham made a switch at the break, introducing Tom Eaves for Wilkinson.

James Henry put a good chance wide for Oxford early in the second half, under pressure from a couple of Gills defenders. Obika flicked another half chance wide soon after.

Parker headed wide for Gills and Eaves was unlucky with a strike from the edge of the box, only denied by a good save from Eastwood, seeing the effort late through a crowded area.

There was controversy with 18 minutes left when Parker unleashed a stunning strike, hitting the woodwork and looking like it had crossed the line before being cleared for a corner. The officials weren’t convinced, however, waving play-on.

Ogilvie had his hands full with the introduction of Oxford debutant Malachi Nappa, making a good block to deny the youngster with 10 minutes left.

With the game seemingly heading for a penalty shoot-out, Mowatt struck from outside the box, past Nelson in the first minute of stoppage-time.

Gillingham: Nelson, Lacey, Ehmer, Nugent, Ogilvie, Clare, Byrne, Wagstaff, Martin (Cundle 61mins), Wilkinson (Eaves 46mins), Parker (Oldaker 77mins). Subs not used: Arnold, O’Neill, Hessenthaler, Simpson.

Oxford: Eastwood, Martin, Ledson, Payne, Ruffels, Henry (Nappa 65mins), Obika, Ricardinho, Mowatt (Baptiste 92mins), Mousinho, Carroll. Subs not used: Shearer, Tiendalli, Williamson, Ashby, Roberts.

Attendance: 1,224 (62 away)