His team held a deserved half-time lead thanks to Robbie Keane's early strike and at that stage the Reds looked good value to continue their 100 per cent start to their Champions League group campaign.
But it was not to be as the unmarked Simao Sabrosa slotted home an 83rd-minute equaliser for Atletico at the Vicente Calderon Stadium to leave both sides with seven points from their opening three games.
"I think we had control of the game in the first half and part of the second half and I'm disappointed because we had chances to finish the game off," Benitez said.
"We then made a mistake in the 83rd minute and we paid for it.
"If you said to me before the game that we would have seven points it might have been good, but after leading until the 83rd minute and the chances that we had, in my opinion we have lost another two points."
He continued: "We didn't have one or two of situations, we had plenty of them on the edge of the box and we didn't finish them off.
"I think we have played a very good match, we have controlled the match and when you play well the other team looks worse.
"I think the entrance of Kun (Aguero) gave more depth to their play and we defended worse, and they also took advantage of the favourable wind in order to play long passes against us."