The rare rebuke came after Mr Putin said the resolution resembled "medieval calls for crusades".
Mr Medvedev said such comments could "lead to a clash of civilisations".
The UN resolution, which Russia abstained from voting on, authorised military action in Libya to protect civilians from pro-Gaddafi forces.
Mr Medvedev told Russian news agencies: "Under no circumstances is it acceptable to use expressions which essentially lead to a clash of civilisations, such as 'crusade' and so on.
"It is unacceptable. Otherwise, everything may end up much worse compared to what's going on now."
Mr Putin had said UN Security Council Resolution 1973, which was adopted on Thursday, was "defective and flawed" as it "allows for everything".