The Reds fielded a young side for their trip to Russia and were punished when Lacina Traore struck in first half injury time to knock Liverpool off top spot.
Young Boys, whom they beat 5-3 in Switzerland, visit Anfield in a fortnight but even a win may still not guarantee progress if the other result goes against them before the final trip to face Udinese next month.
But Rodgers felt the team, which contained nine Englishmen, a debutant in Conor Coady and had an average age of just under 24, had performed well, saying: "Not at all. I think that is a little disrespectful to the players who are here. They have been magnificent and I thought they did really well and we just got punished for a mistake."
He went on: "That led to us losing the game but I don't think it was anything to do with Suarez, Gerrard, Joe Allen, Martin Skrtel or Daniel Agger not being here.
"It was just one of those things. We will take it as a team, we are disappointed but there are so many positives from tonight."
Traore's goal came when he turned Sebastian Coates and lobbed goalkeeper Brad Jones.
Rodgers said the players knew what went wrong and he felt the team he picked had justified his selection.
"We are disappointed with the result. I thought the players put everything into the game," he added. "Tactically our concentration was very good. We controlled the game for 44 minutes and 50 seconds of the first half
"We made a bad mistake and got punished and that is the level.
"It was more of the same second half. We had chances and there is real disappointment in the changing room and I felt for the players. We were up against a good side with top players and we held our own."