The Northern Irishman raised eyebrows with his team selection for the UEFA Champions League clash on Tuesday, dropping a number of first-team regulars to the bench.
Yet Rodgers, who revealed captain Steven Gerrard had undergone a scan a day before the match, insists he set up his side to win the match.
"I put out the best team on Tuesday that could get a result," he said. "My players were magnificent, I think the criticism is a disservice to them.
"We had a gameplan against the best team in the world right now, to stay in the game, control. We then opened up the game with the subs.
"The idea was to be in the game still after 65 minutes, which we did, then use Steven's passing ability, Raheem's [Sterling] pace and [Philippe] Coutinho's creativity.
"I was very proud of the players and the supporters - over 4,000 of them there giving the team a great backing. The criticism is unfair.
"To call Kolo Toure, Lucas Leiva or Adam Lallana a 'reserve'? Those players deserve more praise than that.
"I know in my heart that I make decisions in the best interest of Liverpool Football Club. The performance spoke louder than any words I can say."
Liverpool host unbeaten leaders Chelsea in the Premier League on Saturday, but continue to be without Daniel Sturridge (calf), who was not fit enough for an England call-up on Thursday.
"Daniel Sturridge was out on the field with the rehab team today, but he's still a way off returning," added Rodgers.
