The Kremlin said Putin had called Rouhani to discuss the Syrian crisis as well as a new round of talks about the nuclear stalemate that is set to begin in Geneva on Wednesday.
"Putin stressed that a real chance has now emerged for finding a solution to this longstanding problem," the Kremlin said in a statement.
The Kremlin added that Rouhani gave a "high grade" to Russia's role at the so-called P5+1 negotiations that besides Iran include the five permanent UN Security Council members and Germany.
The terms of the potential deal have been vehemently opposed by Israeli Prime Minister Benjamin Netanyahu and some powerful members of the US Congress.
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Netanyahu, who views a partial suspension of sanctions as detrimental to the negotiations, outlined his opposition to the agreement during talks with French President Francois Hollande yesterday.
The Israeli head of state will continue his diplomatic offensive when he meets Putin in Moscow on Wednesday and receives US Secretary of State John Kerry on Friday.
Russia's top diplomat said "certain critical statements" about the mooted agreement with Iran were "divorced from reality".
"In Geneva, Iran was ready to move further and faster than the steps the (P5+1) was calling for at the start of the year," Lavrov said in comments posted in today's Internet edition of the government-run Rossiyskaya Gazeta daily.
Lavrov added that "those who suspect Russian, American and other participants of the process" of allowing dangerous loopholes in the agreement of "disrespecting our intellectual capacities and our political principles."