Matty Blair, the matchwinner in the semi-final second leg against Mansfield, was again the hero, scoring the winner in the 47th minute.
That came after York had fallen behind to a goal after just 75 seconds, when Luton’s Andre Gray caught the Minstermen defence cold.
York - who last week won the FA Trophy final at Wembley - took a while to get to grips with the game but levelled on 26 minutes with a fine goal from Ashley Chambers.
Blair then struck the winner two minutes into the second half, although it appeared he did so from an offside position.
After that York witheld a barrage of Luton pressure to hang on until the final whistle, much to the delight of their 8,000 fans inside the national stadium.
The win caps a tremendous week for York, who as well as winning the FA Trophy, also gained approval from council chiefs for a 6,000-seater stadium at Monks Cross.
It also comes just 18 months after Gary Mills inherited a squad battling at the wrong end of the Conference table.
For full report, reaction and pictures read Sports Monday, free inside tomorrow’s Yorkshire Post.