The rare rebuke came hours after Mr Putin criticised the resolution, which authorised military action to protect Libyan civilians.
Mr Putin said the resolution resembled "medieval calls for crusades".
Russia abstained from voting on the resolution, under which air strikes are being carried out on Libyan targets.
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. Everyone should remember that."
Mr Putin had said UN Security Council Resolution 1973, which was adopted on Thursday, was flawed as it "allows for everything".
The resolution authorises "all necessary measures" to protect civilians in Libya.
Mr Putin and Mr Medvedev's comments are the most public sign so far of a split in Russia's political leadership.
Mr Medvedev has traditionally been seen as "Putin's man", and many had expected him to return his title to the former President Putin at elections next year.
Analysts have suggested that Mr Medvedev is attempting to position himself as a modernising force in the run-up to the elections.
But in November last year, Mr Medvedev warned that Russia risked slipping into a period of political "stagnation" by being dominated by the pro-Kremlin United Russia party.
Neither Mr Medvedev nor Mr Putin has publicly declared their intention to run for the presidency.