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Ebbsfleet's return to the Blue Square Premier Division ended in disappointment despite taking the lead in the closing stages.
York City emerged 2-1 winners at Stonebridge Road thanks to two goals from striker Jason Walker in the last 10 minutes.
A cagey first half saw few chances created by either side, but Ebbsfleet would have been pleased with their work rate in their first game back at this level.
The game looked to be heading away from Liam Daish's side when Tom Phipp saw red on 68 minutes for an ill-timed challenge. The referee took his time over the decision and eventually gave the midfielder his marching orders.
But, Ebbsfleet substitute Callum Willock gave his side the lead 10 minutes later when he opened the scoring in bizarre circumstances.
Willock headed down a Michael West corner before York keeper Michael Ingham made a mess of a regulation save under the crossbar and eventually spilled the ball over the line unchallenged.
York responded from the set-back almost immediately when striker Ashley Chambers was fouled by new Ebbsfleet keeper Joe Welch in the penalty area. Fellow frontman Walker stepped up to convert the resulting spot kick on 82 minutes.
Walker then completed a stirring comeback from the visitors to steal all three points in stoppage time. His glancing header from Lanre Oyebanjo's cross beat Welch at the far post.