Blair grabbed his first when he found space in the penalty area and was able to fire into the roof of the net.
He headed in Jamie Reed’s cross for his second of the day to take his total to seven goals in his last six matches.
Lincoln’s Jamie Taylor shot wide from 15 yards and Alan Power was denied by Michael Ingham as the Imps suffered their third successive league defeat.
York manager Gary Mills said: “I thought we were excellent today. We’ve had an issue just lately of conceding early goals and luckily for me they’ve got a clock here that I can look at.
“When it went to 21 minutes I honestly believed we’d go on to win the game.
“We’ve conceded early in a lot of games and it was important for us to keep a clean sheet.”