"Putin expressed support for the Greek people in overcoming the difficulties facing the country," a Kremlin statement said.
The statement said the talks were initiated by the Greek side and the two leaders also discussed "several questions on the further development of Russian-Greek cooperation".
A Kremlin spokesman earlier said that Moscow hoped Athens could reach a compromise with its creditors after Greeks rejected further austerity measures in Sunday's referendum.
Peskov added that the Kremlin respected the results of the plebiscite -- which saw more than 61 percent of voters reject a bailout plan -- and would closely follow the events unfolding in the European Union member state.
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Greece's left-wing leadership has made of show of drawing closer to Moscow in recent months as the spat with its creditors has grown more ugly.
Moscow is currently locked in its own standoff with the European Union over the crisis in Ukraine.