The Reds were leading through Dirk Kuyt's first-half strike when substitute John Arne Riise headed into his own net in the fifth minute of added time.
Benitez was also upset by the stream of free-kicks awarded by the official - who also refereed Liverpool's group stage home defeat by Marseille - against his side.
He said: "It was a difficult match and I was very disappointed with the referee. This was not the first time.
"We knew what to expect because we'd had him before against Marseille. He gave just one minute injury-time in the first period and four in the second. It was hard to understand.
"All the free-kicks seemed to go against us. The first four free-kicks against us were for pushing, and then when one of their players (Ashley Cole) pushes one of our players in the back with both hands in the box, there's nothing.
"But we cannot blame the referee for our missed chances. We had at least four clear opportunities, and we must score those.
"But we must now be positive and clear our minds. If we play like that at Stamford Bridge next week and take those chances, we will go through.
"We have confidence in ourselves. I am confident we can do it, I will recall the first 20 minutes of the second period when we were very much on top of Chelsea. If we can do that again at Stamford Bridge, we can still get to the final."