The proposal presented to the rebels in Astana delineates four zones in Syria where front lines between the government and rebels would be frozen and fighting halted, according to a statement made by rebels.
The two leaders met only hours after Mr Putin discussed the plan for safe zones in Syria with United States president Donald Trump in what the White House described as a "very good" phone call.
The agreement, which a Russian delegate said would go into effect on Saturday, is the latest attempt to reduce violence in the Arab country.
To advance his proposal, President Trump will send a senior US official to an upcoming round of peace talks in the Kazakh capital of Astana this week.
Netanyahu subsequently denied reports Moscow had told Israel to end airstrikes in Syria, vowing that the IDF would continue attacking weapons convoys.
Relations between Moscow and Ankara deteriorated after Turkey shot down a Russian warplane at the Syrian border in November 2015 and Russia responded with trade and tourism sanctions.
Relations between Russian Federation and Turkey have also improved greatly, despite the two countries supporting opposites sides in Syria.
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He spoke at a press conference shortly after delegations of the three sponsor nations signed the agreement in the presence of the U.N. Syria envoy, Stafan de Mistura. The U.S. military action sparked new tensions between Washington and Moscow, with top U.S. officials sharply condemning Putin's continued support for embattled Syrian leader Bashar Assad.
The new, Russian-backed version appears meant to be fully demilitarized, as a way of keeping the growing number of warring factions in Syria away from one another.
A senior White House official later confirmed to ABC News that Trump and Putin discussed the possibility of a meeting, but says the two did not commit to anything.
The Syrian armed opposition suspended its participation in the two-day talks on Wednesday and demanded an end to government bombing of areas under its control.
Netanyahu said shortly after Russian Federation entered the war, he told Putin Israeli forces would continue to act against "the transfer of very risky weapons from Iran by way of Syria to Hezbollah in Lebanon".
Putin said that the proposed zones would also be no-fly areas if fighting on the ground there stopped entirely.
Speaking in Ankara before traveling to the Russian Black Sea city of Sochi to meet Putin, Erdogan told reporters that reaching a political solution to the conflict in Syria was a joint goal of Turkey and Russia.
"We can not think about any alternative and we should not have to think of it", Putin said at a press conference.