The Brazilian centre half was adjudged by referee Riley to have blocked Boro striker Joseph Desire Job, a decision which the former Sheffield Wednesday and Chelsea man feels was harsh.
"It was a harsh decision on the penalty. Job's movement was very quick and in my view I touched the ball, I didn't block him" Thome said
"You could say it was a 50-50 but I did not think the referee was in a right position to make that decision. That was a turning point in the game, when you go 2-0 down so early in a final it is hard to get back"
Thome beleives that with a bit more luck Bolton would have got something out of the game and recalls that in seven years in England that yesterday was the first time he had given away a penalty.
"I have played more than 150 games in England and can never remember giving away a penalty before. We kept battling away and I am sure our fans will appreciate that. We never gave up but luck was not on our side"
Centre back Thome, signed from Sunderland earlier in the season also beleives that referee Riley should have evened things up late on when Bolton substitute Stelios Giannakopoulos saw his goalbound effort handled by Boro defender ugo Ehiogu in the area.
"You have to balance things up when it is a 50-50 situation, it was a clear handball by Ehiogu" Thome added