Fighting over the breakaway region between majority-Muslim Azerbaijan and Christian Armenia has raised fears of a wider conflict involving regional powers Turkey and Russia.
The Russian ministry said both confirmed "readiness for close coordination of the actions of Russia and Turkey to stabilise the situation with the aim of returning the settlement of the Nagorny Karabakh conflict to the channel of peaceful talks".
However, Turkey did not release an official statement on the phone call's contents. A Turkish diplomatic source told AFP that the topic of the discussion was "Armenia's aggression."
Russia's diplomatic statement came after Turkish President Recep Tayyip Erdogan said earlier Thursday that a ceasefire was only possible if Armenian-backed forces withdrew from the separatist region and the rest of Azerbaijan.
Ankara has backed Azerbaijan in the conflict and on Tuesday the Armenian defence ministry said a Turkish F-16 flying in support of Baku's forces had downed an Armenian SU-25 warplane.
"The way for a lasting ceasefire in this region depends on Armenians' withdrawal from every span of Azerbaijani territory," Erdogan said in a televised address. Russia, which is in a military alliance with Armenia but also has good ties with Azerbaijan, has made repeated calls for a ceasefire and offered to act as a negotiator. Moscow's UN Ambassador Vasily Nebenzya at a briefing Thursday denied that Russia and Turkey-backed different sides in the conflict.