Earlier this month, Mr Erdogan said that ministerial-level gatherings among the three nations should be arranged, to eventually end with a trilateral meeting involving himself, Mr Putin and Syrian President Bashar Al Assad.
Turkey and Syria have had no official diplomatic ties in 11 years, since the war in Syria began.
The meeting between Russian Defence Minister Sergei Shoigu, Turkey's Hulusi Akar and Syria's Ali Mahmoud Abbas, was held in a “constructive atmosphere”, Turkish state news agency Anadolu reported.
The three officials discussed “ways to resolve the Syrian crisis, the problem of refugees and joint efforts to combat extremist groups in Syria”, the Russian and Turkish defence ministries said.
They “noted the constructive nature of the dialogue held in this format and the need to continue it in the interests of further stabilising the situation” in Syria and the region, Russia's defence ministry said.
Syria also said that the heads of intelligence from Syria and Turkey met in Moscow.
Turkey was considered to be a safe haven for the millions of Syrian refugees escaping the war and the Assad regime.
Turkey has also been alluding to warmer ties with the Syrian government much to the dismay of the opposition that rejected Turkey's calls for the normalisation of ties with the Assad regime.
“There will be no permanent peace otherwise,” he said at the time.
Russia is a staunch backer of the Assad regime but has been mediating between Turkey and Syria, and other parties to the conflict.
Turkey recently launched a military operation against Kurdish targets near Syria's northern border, after a terror attack in Istanbul killed six last month.
Ankara blamed Kurdish militants for the attack, but the US-backed Syrian Democratic Forces denied any responsibility and called for an international investigation into the incident.