This was an interesting situation because this was my game, meaning I'm in charge of making the ruling, yet I'm also one of the players involved in this pot. The ruling I make will essentially decide who wins the tournament (albeit with no way of knowing which way it will go).
To me there were 4 options:
1) Void the hand
2) Let the card stand
3) Pretend it was never there, throw it away, and carry on
4) Shuffle it back into the deck and proceed.
It was an awkward one to call because obviously option 2 is bad for me, option 3 is good, and options 1/4 don't really matter. So obvioulsy I want to make the correct ruling.
So what did I do? I do what I always do and consult Robert's Rules

(I explicitly state that my home games follow RRs)
7. A card discovered faceup in the deck (boxed card) will be treated as a meaningless scrap of paper. A card being treated as a scrap of paper will be replaced by the next card below it in the deck.
Having decided that this is what we were going to do, I confirmed with the other player that this was the ruling and he was happy with it. He was, so we threw the ace to the side and carried on as if it was never there. The end result was I hit a

on the river to make the straight. Had we let the ace play the 55 would of won. In all it was a very unsatisfying way to win a tournament, but I'm quite confident I acted as fairly as I could given the circumstances.
As an aside, GUKPT rules differ here:
# A boxed card will remain in the deck (all players will be made aware of the card) until it comes into play at which point rule 12 will be applied. If the card does not come into play no action will be taken.
Prior to completion of the betting a card exposed in error by the dealer will be shuffled back into the remaining live deck, this applies to the first card of the flop, turn and river cards.
Which I believe is option 4 listed above.