Carruthers's goal booked York's second trip to Wembley in 12 months
A strike from Chris Carruthers sealed York's place in the play-off final, and condemned Luton to another season in the Blue Square Premier.
Carruthers poked in a rebound after Luton keeper Mark Tyler parried Michael Rankine's sweetly-struck free kick.
Liam Hatch and Tom Craddock had chances for Luton but it was a lost cause after Adam Newton was red carded late on in a game marred by crowd trouble.
York meet Oxford in the final, who beat Rushden and Diamonds 3-1 on aggregate.
Visiting players had to run for cover after the match as home fans invaded the pitch and hurled objects, reported to include bottles and coins.
The Hatters had started the game nervously, still smarting from Richard Brodie's last-minute winner in the first leg.
The York striker looked to inflict more misery on his Bedfordshire counterparts with a vivacious display up front, while Rankine was a nuisance, using his big frame to flick the ball forward at every opportunity.
Kevin Gallen almost struck a precious aggregate equaliser for the home side, but keeper Michael Ingham produced a fantastic save to deny the former QPR man.
It was the lively Claude Gnakpa who looked like Luton's most likely source of a goal in the first half, but his threat was nullified firstly by an offside flag, and then by a Luke Graham block on a goalbound shot.
York kept their nerve, however, and confirmed their place in the play-off final when Rankine struck a ferocious free kick that Tyler could only deflect into the path of Carruthers who followed up to send the visiting fans into raptures.
The Minstermen reverted to a backs-to-the-wall display to deal with the Luton siege that came courtesy of a header and a shot from Hatch, and also the dangerous Craddock who was denied by David McGurk's beautifully-timed challenge.
Defender Newton was then sent off for verbally venting his frustrations, allowing York to see out the closing stages in comfort, with a return to the Football League for the first time since 2004 now just a single match away.
Luton manager Richard Money told BBC Three Counties Radio: "I genuinely felt we needed to win at York.
"We played well in the first half but they defended terrifically well. Then we lost a goal straight after half time, which made life very difficult.
"In the end we've come up a little bit short.
York striker Richard Brodie told BBC Radio York:
"I think it's still sinking in a little bit. I've never experienced anything like that in my life.
"As I'm talking now there are still hairs on the back of my neck standing up.
"What a great, great feeling that was. The game where we scored on Thursday might just have kicked the stuffing out of them.
"But today, like we have done all season, we've come here and defended."
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