ALEX Mowatt’s stoppage-time strike sent Oxford United into the Checkatrade Trophy third round after a closely-fought clash at Gillingham.

The U’s had to do it the hard way, falling behind to Mark Byrne’s early penalty as the hosts made all the early running.

But Gillingham squandered chances to move further clear and when they came back into the game, Jack Payne’s classy finish got them back on level terms.

Both sides had chances to go in front in a scrappy second half – and Gillingham appeared to have a legitimate goal ruled out when Josh Parker’s shot bounced down off the crossbar.

United survived and with the threat of penalties looming, Mowatt struck in the 91st-minute to settle the tie.

It moves them into the last-16 next month, three wins from the final at Wembley.

Canice Carroll was handed a start as one of five changes and was quickly into the action, having a shot saved by Stuart Nelson in the second minute.

It was the highlight of an otherwise sluggish start for the visitors, who looked desperately rusty in their first game for ten days.

While Pep Clotet’s side were getting last week’s training camp in Spain out of their system, Gillingham could have been out of sight.

The hosts, who played on Saturday, looked far sharper and cut through at will.

Josh Parker was at the heart of everything and he came close to a fourth-minute goal, but he dragged a shot wide after turning John Mousinho inside out.

Gillingham kept pouring forward and led five minutes later, when Byrne despatched a penalty after Ricardinho brought down Scott Wagstaff.

It should have been 2-0 within seconds. Mousinho’s careless ball across the box went straight to Conor Wilkinson, who was so surprised his first touch was loose and allowed Simon Eastwood to race out and smother.

Another poor pass, this time from Ricardinho, presented a chance to the hosts, but this time Mousinho scrambled back to win the ball back.

Aaron Martin made a vital block on Parker before United’s 62 travelling fans finally saw their side click into gear.

Fortunate to only be one goal adrift, they gradually played their way back into the game.

Nelson stood up well to deny James Henry, whose run had been well found by Jon Obika.

Carroll was a willing runner on the right flank and his industry was key in United’s equaliser, on 31 minutes.

The full back linked well with Henry to whip in a dangerous ball for Alex Mowatt to head over. Referee Charles Breakspear awarded a corner, which was cleared off the line by Byrne.

United kept the ball and Mousinho’s cross-field pass found Carroll to play in Payne. The on-loan midfielder did well to adjust his feet, before curling a shot into the far corner from 12 yards.

The visitors started the second half brightly. Henry could only prod Mowatt’s terrific low cross wide from six yards, while Obika flicked another delivery wide.

United gave a senior debut to Malachi Napa, who was clearly not short on confidence with the way he had tried his luck from 30 yards with a shot which flew over.

But Gillingham came back strongly and Eastwood was needed to make an excellent save to parry substitute Tom Eaves’s strike from a corner.

The U’s goalkeeper was left clawing at thin air two minutes later when Parker unleashed a thunderous 25-yard effort which smashed the woodwork and bounced down. Gillingham were convinced it had crossed the line, but the officials disagreed.

Steve Lovell’s side looked the more likely winners late on, but as the game reached stoppage-time a penalty shoot-out loomed.

Mowatt had other ideas, though.

A minute into stoppage-time he collected a pass from Napa and from 25 yards he fired across Nelson and into the far corner.

Gillingham (3-5-2): Nelson, Lacey, Ehmer, Nugent, Clare (Oldaker 77), Byrne, Wagstaff, Martin (Cundle 61), Ogilvie, Wilkinson (Eaves HT), Parker.

Unused subs: Arnold, Simpson, O'Neill, Hessenthaler.

Booked: Nugent.

Oxford Utd (4-2-3-1): Eastwood, Carroll, Martin, Mousinho, Ricardinho, Ledson, Ruffels, Henry (Napa 65), Payne, Mowatt (Baptiste 90), Obika.

Unused subs: Shearer, Tiendalli, Williamson, Ashby, Roberts.

Booked: Carroll, Mousinho.

Referee: Charles Breakspear (Surrey).

Attendance: 1,224 (62 visitors).