"We made crystal clear that, at a minimum, the priority here should be the safe operation of the air crews over Syria," Pentagon spokesman Peter Cook said.
Two Lebanese sources told Reuters hundreds of Iranian troops had reached Syria in the past 10 days with weapons to mount a major ground offensive. They would also be backed by Assad's Lebanese Hezbollah allies and by Shi'ite militia fighters from Iraq, while Russia would provide air support.
"The vanguard of Iranian ground forces began arriving in Syria -soldiers and officers specifically to participate in this battle. They are not advisers ...we mean hundreds with equipment and weapons. They will be followed by more," one of the sources said.
So far, direct Iranian military support for Assad has come mostly in the form of military advisers. Iran has also mobilized Shi'ite militia fighters, including Iraqis and some Afghans, to fight alongside Syrian government forces.
Moscow said it had hit Islamic State positions, but the areas it struck near the cities of Hama and Homs are mostly held by a rival insurgent alliance, which unlike Islamic State is supported by U.S. allies including Arab states and Turkey.
Hassan Haj Ali, head of the Liwa Suqour al-Jabal rebel group that is part of the Free Syrian Army, told Reuters one of the targets was his group's base in Idlib province, struck by about 20 missiles in two separate raids. His fighters had been trained by the CIA in Qatar and Saudi Arabia, part of a programme Washington says is aimed at supporting groups that oppose both Islamic State and Assad.
"Russia is challenging everyone and saying there is no alternative to Bashar," Haj Ali said. He said the Russian jets had been identified by members of his group who once served as Syrian air force pilots.
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The group is one of at least three foreign-backed FSA rebel factions to say they had been hit by the Russians in the last two days.
At the United Nations, Russian Foreign Minister Sergei Lavrov told a news conference Moscow was targeting Islamic State. He did not specifically deny that Russian planes had attacked Free Syrian Army facilities but said Russia did not view it as a terrorist group and viewed it as part of a political solution in Syria.
The aim is to help the Syrian armed forces "in their weak spots", said Kremlin spokesman Dmitry Peskov.
Pentagon spokesman Peter Cook described Thursday's military talks as "cordial and professional." During the talks, Elissa Slotkin, an acting assistant U.S. secretary of defense, "noted U.S. concern that areas targeted by Russia so far were not ISIL strongholds." Cook said, using an acronym for Islamic State.
The Pentagon said it would not share U.S. intelligence with Russia and suggested the talks included ideas to increase safety, such as agreeing on radio frequencies for distress calls and a common language for communications.
U.S. Republican Senator John McCain, chairman of the Senate Armed Services Committee, and a frequent Obama critic, questioned the logic of talks on how to keep U.S. and Russian militaries apart, known in military parlance as "deconfliction."
"Unfortunately, it appears 'deconfliction' is merely an Orwellian euphemism for this administration's acceptance of Russia's expanded role in Syria, and as a consequence, for Assad's continued brutalization of the Syrian people," McCain said.
Russia's decision to join the war with air strikes on behalf of Assad, as well as the increased military involvement of Iran, could mark a turning point in a conflict that has drawn in most of the world's military powers.
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With the United States leading an alliance waging its own air war against Islamic State, the Cold War superpower foes, Washington and Moscow, are now engaged in combat over the same country for the first time since World War Two.
They say they have the same enemies - the Islamic State group of Sunni Muslim militants who have proclaimed a caliphate across eastern Syria and northern Iraq.
But they also have different friends, and sharply opposing views of how to resolve the 4-year-old Syrian civil war, which has killed more than 250,000 people and driven more than 10 million from their homes.
Washington and its allies oppose both Islamic State and Assad, believing he must leave power in any peace settlement.
Washington says a central part of its strategy is building "moderate" insurgents to fight Islamic State, although so far it has struggled to find many fighters to accept its training.
Moscow supports the Syrian president and believes his government should be the centerpiece of international efforts to fight the extremist groups.
It appears to be using the common campaign against Islamic State as a pretext to strike against groups supported by Washington and its allies, as a way of defending a Damascus government with which Moscow has been allied since the Cold War.
The Russian strikes represent a bold move by President Vladimir Putin to assert influence beyond his own neighborhood. It is the first time Moscow has ordered its forces into combat outside the frontiers of the former Soviet Union since its disastrous Afghanistan campaign in the 1980s.
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The Russian and Iranian interventions in support of Assad come at a time when momentum in the conflict had swung against his government and seem aimed at reversing insurgent gains.
Prime Minister Haidar al-Abadi of neighboring Iraq, where Washington is also leading an air war against Islamic State while Iran aids government forces on the ground, said he would be open to Russian strikes as well.
A Syrian military source said on Thursday that Russian military support would bring a "big change" in the course of the conflict, particularly through advanced surveillance capabilities that could pinpoint insurgent targets.
Putin's gamble of going to war in Syria comes a year after he defied the West to annex Ukraine's Crimea peninsula, drawing U.S. and EU economic sanctions while igniting a wave of popular nationalist support at home.