He said: "I am really disappointed with the situation because we had 100% confidence he would be arriving at Liverpool.
Benitez maintains that his club got a raw deal from the panel that adjudicated on the matter.
"It was a special situation - because we are Liverpool," he said.
"The verdict was a surprise for everyone, our lawyers, the player and his agent. I could not believe it."
Benitez is now considering his options following Heinze's departure to Spain although he is running out of time with the transfer window due to close in eight days.
However he insists his focus at the moment is on the Premier League match against newly-promoted Sunderland at the Stadium of Light on Saturday.
Benitez said: "We need to analyse the situation and look at the squad. It is not easy to find a player of Heinze's quality.
"However for the moment we have to concentrate on the game at Sunderland. That is the important thing."