Those discussions have been possible because Mr. Assad, secure in his support from Moscow and Tehran, no longer sees a fundamental threat to his ability to remain in power. And Mr. Trump’s decisions amounted to an acknowledgment that no escalation of the program, which began in 2013 in concert with the C.I.A.’s counterparts in Saudi Arabia, Turkey and Jordan, was likely to yield a different result.

When it began, the initial objective was to force Mr. Assad to the bargaining table, in a series of negotiations that the secretary of state at the time, John Kerry, took up in earnest in late 2015. But each agreement — for cease-fires, and deadlines for a political “road map” for elections in the country — fizzled. Mr. Kerry fumed that Mr. Obama was not willing to provide the kind of military pressure on Mr. Assad that might bolster the diplomacy. Mr. Obama, for his part, was leery of entering another Middle East war whose outcome he could neither control nor predict.

The program became less relevant as the Russians increased their presence in Syria, targeting and badly weakening the C.I.A.-backed rebels, who were the most capable of the opposition fighters. That helped the Assad government claw back and consolidate territorial gains.

“This is a big deal, but it’s been a long time coming,” Charles Lister, a Syria analyst for the Middle East Institute in Washington, said. “It’s the biggest indication so far of the administration’s having given up on the opposition.”

“After all, the Southern Front has consistently been our most reliable anti-Assad partner,” Mr. Lister said, referring to opposition forces fighting Mr. Assad in the southern part of the country. “It’s also the result of strong Jordanian pressure, as Amman has been pushing a freeze for a long time. So it was probably inevitable, but it’s nonetheless very significant.’’

He added that it was “a big mistake in my mind.”

Other independent experts said it was unclear whether Mr. Trump’s decision would have an impact on fighters defending areas held by the opposition.

At its height, the program was run through operations rooms in Jordan and Turkey, supporting rebel groups fighting under the banner of the Free Syrian Army who were deemed not to be extremists.