Obama's comments at the end of the Group of 20 meeting of the world's largest economies came after Russian President Vladimir Putin said only the Syrian people have the right to decide whether their leader, Bashar Assad, steps down.
Putin told a separate news conference that only some Syrians "who are represented by the armed position" want Assad to step down.
"It's my personal belief, and I shared this with them, I don't see a scenario in which Assad stays and violence is reduced," Obama countered.
While Obama said Russia and China recognize the dangers of all out civil war in Syria, "I wouldn't suggest that at this point the United States and the rest of the international community are aligned with Russia and China in their positions."
Obama met with Putin and Chinese President Hu Jintao on the sidelines of an economic summit. Syria was a top subject.
China and Russia have close ties to Syria and have vetoed two U.N. resolutions that mentioned the threat of sanctions against President Assad's regime. China and Russia, however, did support an observer mission in Syria and a plan by special envoy Kofi Annan to end the violence.
Putin and Obama agreed in bilateral talks Monday that Syrians should choose their own next government, indicating a subtle shift for both.
"It's important to arrive at such a situation" through negotiations among groups in Syria, Putin said Tuesday. "The security and interests of all parties should be agreed upon, not like some countries in North Africa, where violence still continues, despite a regime change."
Since the start of the anti-Assad uprising in March 2011, the regime has responded to unrest with brute force, dispatching snipers, troops and tanks to quash dissent. Activists say more than 14,000 people have been killed since, many of them civilians.
In general, the violence has not stopped the uprising, emboldening protesters, galvanizing international condemnation and leading many in the opposition to take up arms.
Putin said Russia and the U.S. still differ on many issues after talks during the G-20.
He also sees no immediate solution to a U.S-Russian dispute over a missile-defense shield the U.S. wants to set up in Europe.
"It will not be settled, the missile-defense problem, irrespective of whether Obama is going to be reelected or not," he said. "To drastically change it, it would take the U.S. to agree with our proposal," to share control of the system.
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