Hollande said both Russia and France had the same goal to bring peace while avoiding the collapse of Syria but differed in particular on the role of President Bashar al-Assad in a power transfer.
"We have the same objective - to avoid disintegration of this country and to avoid allowing terrorists to profit from this chaos. We want political dialogue," Hollande said, after his first trip to Russia as president.
But he added: "There is the question of the manner of how to get there through political dialogue."
Putin said the French leader brought with him to Moscow new proposals on how to solve the two-year conflict in the Middle Eastern country but quipped that reconciling their countries' positions would be hard without copious amounts of alcohol.
"We had a very active debate and even argued when it came to some issues," Putin said.
"It seemed to me a good bottle of wine - even vodka - would be needed to sort this out," Putin told a news conference to laughter from officials. In an effort to play along with his host, Hollande quipped that he would prefer a bottle of port.
France has been one of the strongest international backers of urgent action to bring about a power transfer in Syria that excludes Assad and can end a conflict that according to the United Nations has claimed 70,000 lives.
Russia has denied it has a policy of propping up Assad, a long-term ally, but has not backed calls for him to stand down, saying this must be the Syrians' decision.
Without releasing details, Putin said that during the talks Hollande had formulated new proposals on the Syrian conflict, adding he was in favour of them being discussed together with other world powers.
"I think we need to heed our partners' opinion on some aspects of this difficult problem," Putin said.
The two men had met once before in Paris last June when their differences on the Syria conflict were laid bare in a news conference after the talks.
After their meeting Thursday, the two leaders were keen to play up the cordial atmosphere as Hollande sought to find the same personal chemistry with Putin that existed with his predecessor and vanquished rival Nicolas Sarkozy.
Hollande thanked Putin for Russia's support for France's military operation in Mali, while Putin said he and his French guest were free to discuss any
Human rights avoided
The French president however appeared to tiptoe around the controversial issue of human rights, saying his duty was to state facts but not to judge.
Human Rights Watch had urged the French leader in the run-up to the visit to press Putin on the rights situation after the worst year for "human rights in Russia in recent memory".
Later Thursday, Hollande was scheduled to meet with several prominent rights activists including representatives of top rights watchdog Memorial and editor of fiercely anti-Kremlin magazine The New Times.
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Putin, addressing the widespread criticism of violations of human rights in Russia, dismissed the issue, pointing to tensions during the electoral campaign that saw him return to the Kremlin for a third term in May.
When challenged by a reporter to comment on a seeming lack of a particular warmth between him and Putin, Hollande said curtly: "I will leave it up to you take the temperature of our relations."
The French president also attempted to make light of the Depardieu furore, without specifically naming the now infamous French tax-exile.
When asked about giving French visas to Russian investors Hollande said: "We must limit immigration but that should not discourage a Russian investor or an entrepreneur, even artists or other famous people from coming to France.
"We don't stop anyone from coming to Russia," Hollande added to much laughter.