Obama announced his decision in an interview with ABC News on the eve of a meeting of Syrian opposition leaders and their international allies in Morocco, but he stopped short of authorizing U.S. arming of rebels fighting to overthrow Assad.
"It's a big step," Obama said in a step that could provide a diplomatic boost to the anti-Assad political cause after nearly two years of fighting.
France, Britain, Turkey and the Gulf states led the way last month in recognizing the opposition coalition. But Washington held off until now, demanding the groups, dogged by splits and rivalries throughout their battle to end the Assad family's long authoritarian rule, do more to coalesce into a unified front.
A formal endorsement by Obama, accused by critics of failing to respond forcefully enough to the bloody Syrian conflict, could mark a new phase in his efforts to isolate Assad, who has defied repeated U.S. calls to step down.
But little in the way of direct military or financial support is expected to be channeled to the coalition at the Morocco meeting on Wednesday, partly because it lacks the ability to act as a provisional government and because Western powers are still wary of backing Islamist fighters in the rebel ranks.
The diplomatic designation - which had been widely expected - could open the door to further U.S. non-lethal assistance, including communications equipment and humanitarian aid, and deeper political contacts.
But Obama made clear that he remains cautious about some of the armed Syrian factions linked to the political coalition and is not ready to start supplying weapons to the rebels, something he has steadfastly resisted despite demands from some Republican critics.
"Not everybody who's participating on the ground in fighting Assad are people who we are comfortable with," Obama said. "There are some who, I think, have adopted an extremist agenda, an anti-U.S. agenda, and we are going to make clear to distinguish between those elements."
DESIGNATED AS TERRORIST ORGANIZATION
Obama specifically singled out the radical Islamist Syrian group Jabhat al-Nusrah, which the United States on Tuesday designated as a foreign terrorist organization that it said was trying to hijack the rebellion on behalf of al Qaeda in Iraq.
U.S. officials said the al-Nusra group had claimed responsibility for carrying out nearly 600 attacks in major cities that have killed numerous innocent Syrians during the uprising against Assad.
U.S. officials said it was an important signal both to the Syrian opposition and its foreign supporters, particularly in the Gulf, that al-Nusra and its ilk cannot play a part in Syria's eventual political transition.
Tuesday's action came as U.S. officials were set to attend the Friends of Syria meeting in Marrakech, to discuss the Syria crisis, as rebels push forward on the battlefield and move to unify the political opposition.
Rebels clashed on Tuesday with government forces near Damascus airport, battling for the capital's outskirts in a conflict which the United Nations said has driven half a million people from the country since it began in March 2011.
Fighting near the airport, 20 km (12 miles) southeast of Damascus city center, is part of a broader confrontation between the army and rebels who hold a near-continuous arc of territory from the east to the southwest of Assad's power base.
At least 40,000 people have been killed in Syria's uprising, which started with street protests that were met with gunfire by Assad's security forces, and spiraled into the most enduring and destructive of the Arab uprisings.
Stalemate between major powers, particularly the United States and Russia, has paralyzed the wider international response to the violence, leaving regional Sunni Muslim states such as Turkey and the Gulf Arab countries helping the rebels and Shi'ite Iran providing support to Assad.