The Reds surrendered top spot in Europa League Group A to the Russian side as Lacina Traore's first-half strike gave the hosts victory.
But, despite not having the likes of Luis Suarez, Steven Gerrard and Raheem Sterling to call on in Moscow, Rodgers insisted his rotated side were unfortunate to lose.
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"We just got punished for one mistake, otherwise the players who were here did fantastically well, and it wouldn't have mattered if those other players were here. It is just one of those things, and we will have to take from it and learn from it."
The Northern Irishman also looked ahead to next week's home clash with Young Boys, with the Merseyside outfit needing victory to keep their qualification hopes alive.
"We know we have to really focus on the game next week now, because we realise it's one we really need to win," he added.
"It was always going to come down to the last games in this group, and next week is a really big game for us now."