BEIRUT — The Obama administration’s Syria strategy suffered a major setback Sunday after fighters linked to al-Qaeda routed U.S.-backed rebels from their main northern strongholds, capturing significant quantities of weaponry, triggering widespread defections and ending hopes that Washington will readily find Syrian partners in its war against the Islamic State.

Moderate rebels who had been armed and trained by the United States either surrendered or defected to the extremists as the Jabhat al-Nusra group, affiliated with al-Qaeda, swept through the towns and villages the moderates controlled in the northern province of Idlib, in what appeared to be a concerted push to vanquish the moderate Free Syrian Army, according to rebel commanders, activists and analysts.

Other moderate fighters were on the run, headed for the Turkish border as the extremists closed in, heralding a significant defeat for the rebel forces Washington had been counting on as a bulwark against the Islamic State.

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