The centre back was penalised for a foul on Thierry Henry when he shielded the ball from the French striker.
Midfielder Patrick Vieira headed in at the far post after Zinedine Zidane's free kick was deflected across the area.
"For me it wasn't a foul, if anything it was a foul by him (Henry) because he came from behind and collided with me," Puyol told reporters after their second round defeat.
"But referees can get things wrong.
"It was just a shame that the free kick hit the head of one of our players (Xabi Alonso) and then Vieira's header hit another player (Sergio Ramos), the post and then went in.
"It hurts to lose this way, because I think we deserved more and we were playing a great game. But that's football. We now have to recover and think ahead to the next tournament."
CLEVER TACTICS
Puyol said France had played to their strengths and devised a clever tactical
"It was a very intense game and we played some good football in the first half, but their equaliser did us a lot of damage," he said referring to Franck Ribery's 41st minute strike.
"Then after the break they pressured us more, didn't let us play our normal game and the second goal finished us off.
"We played well, but we had a great team against us."
Midfielder Cesc Fabregas bemoaned Spain's failure to live up to their billing once again and said he did not believe France were the better side.
"The expectations were so high and now they are gone," he said. "They closed us down well, they are a very experienced team and we lost. That's it.
"We played the way we know how to play and we played well today but they finished the job better than us.
"But I don't think they are a better side than us. I don't think they deserve to go to the quarter-finals instead of us, but they are France and once again Spain are out early."
France face Brazil in the quarter-final on Saturday.
