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A late penalty knocked Ebbsfleet out of the FA Trophy in Saturday.
Liam King scored the winner after Kenny Clark had been sent off in the 86th minute.
Both sides had chances in Yorkshire and a replay would probably have been fair but referee Ross Joyce punished Clark for an incident in the box and King did the rest.
Fleet boss Jamie Day made three changes to his starting XI at the Eon Visual Media Stadium. One of those was enforced, with Matt Johnson replacing the injured Dean Rance in central midfield. Kelvin Langmead returned in defence, with Dean Pooley making way. Ben Jefford, on loan from Welling, made his debut at left wing-back and Brendan Kiernan dropped to the bench.
North Ferriby were unchanged from their 3-0 home win over Worcester a week earlier.
Gregg Anderson almost got on the end of an early free-kick for the Villagers before Danny Kedwell headed Johnson's deep cross straight at goalkeeper Adam Nicklin at the other end.
Nicklin then made a hash of clearing Anderson's backpass, kicking the ball against Kedwell. The two players turned to see the ball loop across the penalty area, with Nicklin pursuing Kedwell until the danger eventually passed - Jefford's cross drifting beyond the back post.
North Ferriby thought they'd broken the deadlock moments later. Jason St Juste turned away from three Fleet players in midfield and took Langmead out of the game with a through-ball into King's path, which the Villagers skipper planted beyond Edwards into the net. But the assistant's flag, raised for offside, saved the Fleet.
However, the visitors looked uncertain at times, with St Juste a constant menace down Ferriby's left flank.
Ebbsfleet put together a fine passing move which culminated with Johnson's cross from the right being headed wide, from inside the six-yard box, by Theo Lewis.
Physical battles were dominating the contest. Fleet's back three had their hands full with the giant figure of Tom Denton, while at the other end, Adam Cunnington was involved in a running battle with the Villagers' backline.
Kedwell had a shot deflected behind for a corner as the visitors looked to make their attack the best form of defence. Langmead then got his head to Jefford's swirling cross from the left, only for Nicklin to dive low and grab the ball before it could creep inside the far post.
Play switched to the other end once more. St Juste's corner from the right was nodded back across goal by Denton and an ambitious bicycle kick from Danny Clarke dropped onto the roof of the net.
The lively St Juste spun away from Matt Fish too easily inside the Fleet box and got a powerful shot away which forced a smart save from Edwards.
Theo Lewis threw himself in front of a Russell Fry strike as the home side end the first half on top.
But it was Ebbsfleet who came within inches of breaking the deadlock after the restart. The ball looped high in the air inside the Ferriby box and with goalkeeper Nicklin scrambling, it was turned against the inside of the post.
Fleet had another great chance a couple of minutes later. North Ferriby failed to clear their lines following a free-kick and when Johnson helped the ball back into the danger zone, Langmead found himself with a clear sight of goal. But his shot was straight at Nicklin to the relief of the Villagers.
They were thanking their lucky stars again when Cunnington's shot from 20 yards smashed against the crossbar with Nicklin totally beaten, before bouncing down on the goal line.
Fleet were getting on top and Theo Lewis headed over from a Stuart Lewis cross.
But the home side almost made them rue those missed opportunities when Russell Fry curled a free-kick over the wall and against the crossbar. A goalmouth scramble followed and it took some desperate defending from the Fleet to clear their lines.
St Juste then ran 50 yards, beating several players on his way, before crossing for Liam King at the back post. King struck his volley well but it flew into the side-netting.
Now it was Ferriby doing the pressing and King sent another volley just past the post.
New signing Mark Gower, on for his Fleet debut, went down in the Ferriby box but referee Ross Joyce waved away his penalty claims.
Mr Joyce did point to the spot, moments later though, at the other end. He showed Clark a straight red card and King fired a precise penalty into the bottom corner.
Kedwell should have sent the tie to a replay in stoppage-time but he lashed Cunnington's knockdown wildly over the bar.
The officials left the field to a torrent of abuse but North Ferriby cared not.
North Ferriby: Nicklin, Topliss, Wilde (Peat 82mins), King, Anderson (Gray 14mins), Hone, Clarke, Fry, Denton, Bolder (Kendall 79mins), St Juste. Subs not used: Nicholson, D'Laryea.
Ebbsfleet: Edwards, Langmead, Acheampong (Pooley 40mins), Clark, Fish, Jefford (Kiernan 78mins), S Lewis, Johnson, T Lewis (Gower 74mins), Kedwell, Cunnington. Subs not used: Hall, Shields.
Attendance: 610.