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Kenny Clark’s goal was enough to send Ebbsfleet through to round two of the FA Trophy.
Clark headed in the crucial goal after 52 minutes in Tuesday night’s replay to hand Fleet a match against Kidderminster in the next round.
Boss Daryl McMahon was pleased with the 1-0 win and said it could have been even bigger.
“It was a good win and a good performance,” he said.
“We played really well. I thought we could have scored a couple more goals but Brandon Hall (the goalkeeper) was outstanding.
“Garry Hill (the Woking manager) came out after the game and said the only positive thing for them was that it wasn’t two or three so that says a bit about our performance, which was a good one and hopefully we can build on that this Saturday.”
McMahon swapped his front two for the match, with Danny Kedwell and Darren McQueen replacing Charlie Sheringham and Bradley Bubb, but it was their defender Clark who struck the decisive blow.
Fleet bossed the opening stages of the match as they looked to cause an upset against their National Premier opponents. The pair had drawn the first match 1-1 at the weekend.
Nathan Ashmore, in the Fleet goal, made a save from Jake Caprice while at the other end Anthony Cook forced Hall into a save.
McQueen guided a header at Hall before the break and the two sides were all square at the interval.
Fleet started the second half well, with Cook twice coming close. His first effort went narrowly wide and his second was saved by Hall. But from the resulting corner Fleet scored.
Jack Powell took the corner and when Woking failed to clear, Clark was on hand to nod the ball home.
Woking responded and it needed a solid rearguard display from Fleet to keep them out.
Woking dangerman Gozie Ugwu was kept quiet and McMahon praised Clark, saying: “You can see why he has had some attention but our players did well and Kenny Clark handled him very well.
Ugwu’s late effort couldn’t beat Ashmore. Joey Jones put a couple of efforts wide and the Fleet keeper blocked another effort on the line as Woking failed to find a way through.
Ebbsfleet: Ashmore, Cook, Connors, McCoy, Winfield, Clark, Rance, Drury, Kedwell, McQueen (Deering 86mins), Powell (Lewis 79mins). Subs not used: Sheringham, Bubb, Miles. Attendance: 613