Henry told BBC Sport: "We haven't got anything out of the final, despite all our hard work.
"I was kicked all over the place. I expected the referee to do his job. I don't think he did."
Henry also reacted angrily when asked about his future: "Listen, let's talk about some proper questions."
The Frenchman, who was fuming after the game, also felt Samuel Eto's equaliser should have been disallowed for offside.
We can be more than proud but I'm sorry, some of the refereeing was horrendous
Thierry Henry
"I'm not usually a troublemaker, but I've just seen the television and Eto'o's goal was offside.
"It was always going to be difficult to play Barcelona. But with 10 men that is almost impossible.
"Jens probably deserved to be sent off - there is nothing to be said about that. But in the first half Rafael Marquez and Carles Puyol went right through me and they didn't even get a yellow.
"Then I got the ball in front of the bench and Mark Van Bommel kicks me and I end up getting a yellow."
Henry added: "When you see Eto'o is offside it kills you. It kills you because you've been defending and running.
"I was dead after an hour. I was trying to do some stuff when Alex Hleb gave me that amazing ball, I tried to go as far as I could and hit the ball, but I just couldn't.
"It's just sad. You can lose, but to lose like that.
I don't like to be in the position of saying things about the referee but maybe it's true
Cesc Fabregas
"I tried to do what I could and try and defend and try and bring the ball back and help the team, but if they allow an offside goal it is going to be even more difficult.
"Everyone was talking about Ronaldinho before the game. I didn't see him today and I didn't see Eto'o," he said.
"Henrik Larsson made the difference by setting up two goals. That was the key.
"We can be proud, we can be more than proud, but, I'm sorry, some of the refereeing today was horrendous."
Henry's team-mate Cesc Fabregas was equally scathing of the referee after the final whistle.
He added: "You have to be fair in football - you have to be honest and well done to you if you've won, but you have to win in a good way.
"And then you see a player like Marquez who is kicking Thierry all the time or trying to hit him all the time from behind.
"And then Jose (Antonio Reyes) goes to him to get the ball and he just makes theatre of it and goes on the floor to lose time.
"I don't like to be in the position of saying things about the referee but maybe it's true. If you look at the first goal for Barca, it's clearly offside." :|
