It was a cruel way for Everton to lose the match although in truth they hadn't really deserved to win and were largely second best, especially in the first half.
So, the Blues are out of the FA Cup and now have nothing left to focus on but Premier League survival which will surely be a tough test from this point on.
There will probably be two schools of thought on this result.
On the one hand defeat is always tough to take and will potentially further damage fragile confidence with the gruelling league fixture list about to resume.
It might even be psychologicaly advantageous for the Hatters who are locked in that relegation struggle with Everton.
However, perhaps being free of other distractions could work in the Toffees favour leaving them able to concentrate all their efforts on that Premier League battle for survival.
The home side had chances but once again but their striker's struggles continue with neither Dominic Calvert-Lewin or Beto, partnered together up front for the first time, unable to find a goal.
Luton were on top for long periods and led at half-time following Vitalii Mykolenko's thirty-ninth minute own goal.
Everton came out strongly to begin the second half but again were finding it tough to create clear chances with only two shots on target all game long.
But the Blues did find an equaliser as Jack Harrison equalised giving the home supporters hope that their team could turn the tie around.
That proved to be a forlorn hope and right at the death Luton won it as the Toffees defence went to sleep from a set-piece and Cauley Woodrow headed in the winner to enalbe to visitors to repeat the scoreline and result of their league visit to the Grand Old Lady.
In many ways this was a typical cup game with a lot of huff anf puff from both teams and some quality moments with the match ebbing this way and that.
And of course it had the dramatic last-gasp moment which decided the outcome and ended Everton's interest in the FA Cup this season.
Now, let us hope that Sean Dyche's injured players (in particular Abdoulaye Doucoure and Andre Gomes) can return very soon because this side looks well short of the attacking edge without them that will be needed to avoid a repeat of the last two campaigns.