The Minsterman, relegated in 2004, were beaten finalists two years ago, but went one better this time as goals from Ashley Chambers and Matty Blair wiped out Andre Gray's early goal.
Indeed, the 30,000-plus Luton fans were celebrating after just 71 seconds as they enjoyed a dream start when Robbie Willmott slipped in Gray from the left and the striker opened his body and placed a superb effort into the bottom corner.
York could have been flustered, but they responded by bombarding the Luton goal for much of the next 20 minutes.
Jon Challinor almost levelled but his goalbound shot was deflected over by Alex Lawless and then Jason Walker forced Mark Tyler into an athletic save as he tipped over the 18-goal striker's header.
But Gary Mills' men got reward for their total domination in the 26th minute when Chambers rifled in an unstoppable effort from 16 yards following a Lanre Oyebanjo free-kick.
If Luton thought their start to the first half would not be bettered, they were mistaken as York needed just 69 seconds of the second half to take the lead for the first time, though it should have been ruled out for offside.
Oyebanjo launched a long throw into the area, Walker flicked on and Blair advanced a yard past the last defender and tucked home.
Luton were unable to respond in the manner that the Minstermen did in the first half and James Meredith headed over and Chambers brought a save out of Tyler as the Minstermen pushed.
The Hatters eventually stirred and Gray should have levelled, but just three yards out he inexplicably missed his kick twice and York cleared their lines, while some heroic defending from Oyebanjo denied John Kissock.
Luton threw everything forward in the final minutes in a bid to force extra time, but York held firm to seal their return to the Football League.