Liverpool, unbeaten in the Premier League, went behind after their defender Sami Hyypia deflected in a shot from Serdar Ozkan.
Brazilian Bobo increased the lead after the break when he slotted in from inside the area.
Captain Steven Gerrard brought the Reds back into the game with a flying header but his side failed to salvage anything from their trip.
Benitez added: "We had a lot of shots on target and shots off target. We controlled almost everything but made a big mistake in the first half."
Gerrard agreed with his manager and believed the Reds could still qualify from the group although he added they have a "mountain to climb".
"We are pleased with how we played but disappointed with the result. We need to keep going and win the final three games and see what happens," he said.
"We need to take the positives and learn from our mistakes. We are capable of winning our final three games."
"It is the worst possible result. We had a mountain to climb but we have got an even bigger one to climb now.
"Mistakes happen as a result of misunderstandings but they put us under pressure."