Benitez's side appeared to be heading towards a vital victory over Lyon in Group E when Ryan Babel climbed off the bench to net a stunning goal seven minutes from time.
But Lisandro struck in the final minute to earn Lyon an unlikely point and secure their passage into the last 16, while Liverpool could now be knocked out if Fiorentina beat the French side next time out.
But Benitez remained positive after the draw, hailing the performance of his side, if not the result.
He told Sky Sports: "With all the problems that we have, I think that the reaction of the players was very, very positive.
"We could win, we had chances, we were working hard against a good team and we conceded in the last minute.
Really disappointed"So really unlucky, really disappointed but I think the players were doing well."
He added: "We are working so hard, it's a pity at the end. But football is very strange and sometimes you don't have what you deserve.
"But any way, I was pleased for the players because their reaction was good with a lot of difficult situations but really disappointed for the result, not for the performance of the players."
Benitez does not think Liverpool's chances are over, but he conceded his team needed to do 'another miracle'.
"Okay, we have to win now and we have to go to the next game and wait for the result between Lyon and Fiorentina and see if we can win and go to the last game and try to do another miracle."
He added: "I think it will be difficult but still we are alive so we have to keep going."
Keep goingBenitez added his side had to keep going even if they were knocked out of the Champions League.
"If it is not, we have to keep going because it is always the same in football, we have to keep going after one game there is another one."
He also maintained he was still the right man to lead the Reds.
"Always any manager has to be under pressure so I feel it is a question of to be calm and keep going," added Benitez.
"I feel that today the team was again a little bit better and that is a positive message for me."