The spy agency chief said Washington had reason to worry about who might replace President Bashar al-Assad if his government fell, given the rise of the Islamic State group and other jihadists in Syria.
"I think that's a legitimate concern," Brennan said when asked if the US government feared who might succeed Assad.
Speaking at an event at the Council on Foreign Relations, he said that "extremist elements" including the IS group and Al-Qaeda veterans are "ascendant right now" in some parts of Syria.
"The last thing we want to do is allow them to march into Damascus."
"That's why it's important to bolster those forces within the Syrian opposition that are not extremists," Brennan said.
The US military is funding the training and arming of "moderate" Syrian rebel forces but the effort is only now getting off the ground.
Washington's stance is that Assad should have no role in Syria's future but President Barack Obama's administration and other governments wanted to see a political solution that would ensure a representative government, he said.
"None of us, Russia, the United States, coalition, and regional states, wants to see a collapse of the government and political institutions in Damascus," Brennan said.
- IS exploits digital media -
Interviewed before a live audience by PBS television journalist Charlie Rose, the CIA chief also described the viral nature of the threat posed by the Islamic State group, saying it represented a change from previous terror organizations.
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IS is skilled at exploiting social media to spread its propaganda and recruit, enabling it to extend its reach in a way that was difficult to track and deter, according to Brennan.
"ISIL demonstrates a very worrisome development. It has been a phenomenon that has snowballed in terms of its resonance and appeal," he said, using an alternative acronym for the group.
The emergence of the Islamic State extremists in Iraq has seen Washington and Tehran waging war against the same common adversary.
Asked about possible coordination between Iran and the United States against the IS, Brennan suggested the two arch-foes are cooperating indirectly through Iraqi partners to defeat the jihadists.
"There's an alignment of some interests between ourselves and Iran" when it comes to fighting the IS jihadists in Iraq, he said.
"We work with closely with the Iraqi government. The Iranians work closely with the Iraqi government as well," he said.
Brennan also defended negotiations with Iran over its nuclear program, saying the US government has weighed key aspects of a potential agreement with great care.
The talks between world powers and Iran have raised a political firestorm in Washington, with Republican opponents of Obama accusing his administration of preparing to make damaging concessions to Tehran.
But the CIA chief insisted there was no reckless push for a deal.
"This is not something that's being done in any haphazard way," he said.
He added he was confident that the United States and other powers taking part would insist on "minimum requirements that we are not going to reduce."