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Ebbsfleet's interest in their twice-postponed FA Trophy third round tie at York on Tuesday night was ended by Matt Blair's early second-half strike.
Blair, who scored twice when the Fleet lost 3-2 in the league meeting last month, broke the deadlock three minutes after the restart, and the home side also squandered a late penalty.
York's 48th-minute opener proved the key moment when Blair got on the end of a left-wing cross to beat Preston Edwards.
Liam Enver-Marum was denied a rapid equaliser by York keeper Michael Ingham three minutes later and Calum Willock fired over the bar.
Blair was again involved late on, when York were awarded a disputed spot-kick, after Fleet's Joe Howe was ruled to have bought him down, but Jason Walker's kick struck a post.
Fleet responded by winning a corner as the clock ticked down. Edwards raced upfield as an extra attacker but his blushes on the break were then spared by an offside flag.