The leaders discussed "current international issues, including the situation in Syria in the context of preparations for the Geneva 2 conference, and the implementation of agreements on the Iranian nuclear programme," the Kremlin said in a statement that did not specify who initiated the telephone call.
Russia has been one of the principal backers of Iran's inclusion in the Syria peace negotiations, which are due to resume for the first time in more than a year in Switzerland on January 22.
But German Foreign Minister Frank-Walter Steinmeier said he backed Iran's involvement in the conference, which aims to engage representatives of Syrian President Bashar al-Assad and members of the opposition in direct talks for the first time.
Iran has already rejected a US suggestion that it play a "sideline" role at the negotiations, calling the proposal insulting.
The Iran nuclear talks that resume today in Geneva aim to put into action an interim nuclear deal clinched in November.
Russia has said wants the negotiations to proceed at a faster rate.