The case of Naama Issachar, an Israeli citizen serving a 7.5 year jail sentence in Russia for drug possession, was also raised during the conversation.
Speaking via phone, the two leaders spoke of the continuing need to have deconfliction mechanisms in place to prevent military engagement between Russia and Israel in Syria.
Russia backs Bashar Assad's authoritarian government in the country, and has criticised IDF airstrikes aimed at preventing Iranian entrenchment near the border with Israel.
Israel, meanwhile, has repeatedly stated that it will not tolerate Iran's entrenchment, with the IDF saying it coordinated its aerial campaign with Moscow through the deconfliction mechanisms. Israel has further warned that it will retaliate against any attack staged from Syria.
Earlier in the day Foreign Minister Yisrael Katz met with his Russian counterpart Sergey Lavrov in Rome where the matter was also raised.
"I stressed the need to bring about Iran's withdrawal from Syria, and the fact that Israel will continue to work to safeguard its security interests and prevent Iran's consolidation in the country, while taking great care not to harm the Russian forces that are there," said Katz.
The two also discussed Issachar. Katz requested the Russian authorities allow the Issachar family to visit Naama more often, and hoped that Putin would accept the requests for pardon that had been put to him.
Speaking to Israeli media, Naama's mother, Yaffa Issachar, said: “in our conversation, I asked the foreign minister to thank the prime minister for his continued efforts to free Naama and firmly executing one of the important purposes he has to uphold as Israel’s prime minister - guaranteeing the well being of the Jewish people and the citizens of Israel who might be subject to distress because of their Jewishness or nationality.”
Putin will join French President Emmanuel Macron in Jerusalem in January, at events to mark International Holocaust Remembrance Day. They are expected to comprise the largest ever event with a focus on combating antisemitism.