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A solitary strike from Moses Ashikodi saw Ebbsfleet spring a surprise over play-off chasing York in the Blue Square Premier at Stonebridge Road on Saturday.
There was little to choose between the sides in the first half and the teams went in level at the break.
Ashikodi then struck the only goal of the game after 52 minutes when he drove the ball into the bottom left corner of the goal from edge of the box.
Fleet were the better side in the second half and York were reduced to 10 men after 65 minutes when leading scorer Richard Brodie was sent off.
He was given his marching orders for a foul on Dean Pooley that resulted in the Fleet player needing lengthy treatment for a head injury.
Fleet keeper Lance Cronin denied Courtney Pitt as the home side sent York to their first defeat in 11 league games.
The result put Liam Daish’s (pictured) side seven points clear of the relegation zone, but the teams below them have games in hand.