The winger was York's Wembley hero two years ago when he scored the winner in the Conference play-off final over Luton Town, but he returned to haunt his former employers at Bootham Crescent on Monday.
Blair was on hand to tuck home from close range five minutes into the second half and York were unable to respond in a game that was rearranged after being postponed on Saturday due to a waterlogged pitch.
Nigel Worthington's York side had embarked on a 17-game unbeaten run to seal the final play-off spot after struggling earlier in the season and they will have to come from behind in Friday's second leg at Highbury to deny Blair another trip to Wembley.
Fleetwood, who finished fourth in the table, came close to an opening goal when Antoni Sarcevic tried his luck and Nick Pope was alert to deny him.
York responded and Michael Coulson cut inside from the left and let fly with a shot the flashed past the far post early in the second half.
It was the visitors who took the lead five minutes after the break, though, and Sarcevic was the architect as his ball across the face of goal was met by Blair, who was left with a simple finish at the second attempt.
Things almost went from bad to worse for York when Iain Hume played in David Ball but Pope came out to narrow the angle and did enough to thwart the striker.
Coulson and Calvin Andrew had chances to level the tie, but were off target and Fleetwood will take a slender lead into the second leg as they strive to secure their second promotion in the space of three years.
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