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Gillingham were awarded three spot-kicks in normal time but managed to lose Tuesday’s Carabao Cup game on a penalty shoot-out.
Brandon Hanlan put the Gills ahead with a penalty in the first half but had another spot-kick in the second half saved.
Tristan Abraham got Newport level but both teams scored from the spot at the death, with Padraig Amond cancelling out Mikael Ndjoli’s effort. Newport keeper Nick Townsend saved twice in the penalty contest as Newport won.
Gillingham boss Steve Evans made just three changes to his team, with Connor Ogilvie going into defence and Alfie Jones moving up into midfield.
Newport meanwhile, made nine changes. Their manager Michael Flynn - a former Gills player - had told his fans not to bother travelling to the game. 200-odd ignored the advice to cheer their League 2 side on at Priestfield.
The Gills may have had the words of Steve Evans still ringing in their ears from the weekend and they certainly started brightly on Tuesday. A new midfield two of Alfie Jones and Mark Byrne - a former Newport player - helped the defensive side while the returning Regan Charles-Cook looked like he had a point to prove after being left out on the Saturday.
Mikael Ndjoli put a good chance over the bar early on for the Gills before Charles-Cook curled an effort against the upright.
It was a foul on Charles Cook, by Scot Bennett, that led to Gillingham’s opener from the spot. A shove in the back of the Gills man sent him to the ground and Hanlan’s penalty had too much pace on it to beat keeper Nick Townsend, who had gone the right way.
Townsend turned a 20 yard effort from Alex Jakubiak wide and was then thankful to his defence for making a clearance after the rampaging Charles-Cook had surged into the box.
The visitors hadn't posed too many problems but a couple of chances fell their way. Corey Whitely had had a shot blocked and moments later created a chance for Bennett and keeper Jack Bonham had to be there to make a save.
The Gills deservedly led at the break and came close to a second just before half-time when Townsend turned Hanlan’s header onto the foot of the post after he met a tantalising cross from Charles-Cook.
Newport almost scored early in the second half when Padraig Amond spotted a gap at Bonham’s near post and the Gills keeper only just managed to keep the low shot out.
The visitors had come out fired up and Matty Dolan dragged a long range effort wide.
Gillingham responded and went close when Byrne’s shot was deflected for a corner and Ogilvie headed the subsequent flag-kick wide.
Hanlan had the chance to make it 2-0 from the penalty spot, after he had been fouled in the box by Kyle Howkins. The Gills man went down the middle and keeper Townsend saved with his legs.
Mark O’Brien should have punished the Gills moments later, getting on the end of a free-kick but he headed wide.
The game got scrappy at times as Newport went in search of an equaliser, with the Gills forced into hacking several long balls clear.
Hanlan had another chance to make the game safe after racing onto a long ball forward. He was one on one with the keeper but Townsend made the save and Hanlan hit the follow-up over the bar.
A minute later and Newport levelled as Dolan’s curling free-kick was met by Abrahams. Getting enough on the ball to take it past Bonham.
Gillingham had another lifeline when Mark Byrne was fouled in the box and Ndjoli got the better of Townsend to make it 2-1. It wasn’t enough, however, as Newport were awarded a penalty of their own in stoppage-time and Amond levelled it up.
During the chaos referee Trevor Kettle also sent Gills goalscorer Ndjoli off for a second bookable offence, having been penalised for the penalty.
The game went straight to penalties and Townsend was the Newport hero, saving from Alfie Jones and Mark Marshall, to win the shoot-out 4-1. Mikael Mandron scored for the Gills while John Sheehan, Amond, Mickey Demetriou and Abrahams.
Gillingham: Bonham, Hodson, Fuller, Ehmer, Ogilvie, Jones, Byrne, Ndjoli, Jakubiak (Marshall 70mins), Charles-Cook (Woods 90mins), Hanlan (Mandron 86mins). Subs: Walsh, Tucker, O'Keefe, List.
Newport: Townsend, Leadbitter, Howkins, Stojsavljevic (Amond 28mins), Dolan, Abrahams, Nurse, Bennett (Sheehan 80mins), Whitley, Maloney, O’Brien (Demetriou 90mins). Subs: King, Haynes, McNamara, Ekpiteta.