Officials said the phasing out of the secret program reflects Trump's interest in finding ways to work with Russia, which saw the anti-Assad program as an assault on its interests. The shuttering of the program is also an acknowledgment of Washington's limited leverage and desire to remove Assad from power.
Just three months ago, after the United States accused Assad of using chemical weapons, Trump launched retaliatory airstrikes against a Syrian air base. At the time, U.N. Ambassador Nikki Haley, said that "in no way do we see peace in that area with Assad at the head of the Syrian government."
Officials said Trump made the decision to scrap the CIA program nearly a month ago, after an Oval Office meeting with CIA Director Mike Pompeo and national security adviser H.R. McMaster ahead of a July 7 meeting in Germany with Russian President Vladimir Putin.
Spokesmen for the National Security Council and the CIA declined to comment.
After the Trump-Putin meeting, the United States and Russia announced an agreement to back a new cease-fire in southwest Syria, along the Jordanian border, where many of the CIA-backed rebels have long operated. Trump described the limited cease-fire deal as one of the benefits of a constructive working relationship with Moscow.
The move to end the secret program to arm the anti-Assad rebels was not a condition of the cease-fire negotiations, which were already well underway, said U.S. officials, who spoke on the condition of anonymity to discuss the secret program.
Trump's dealings with Russia have been under heavy scrutiny because of the investigations into the Kremlin's interference in the 2016 election. The decision on the CIA-backed rebels will be welcomed by Moscow, which focused its firepower on those fighters after it intervened in Syria in 2015.
Some current and former officials who support the program cast the move as a major concession.
"This is a momentous decision," said a current official, who spoke on the condition of anonymity to discuss a covert program. "Putin won in Syria."
With the end of the CIA program, U.S. involvement in Syria now consists of a vigorous air campaign against the Islamic State and a Pentagon-run train-and-equip program in support of the largely Kurdish rebel force that is advancing on Islamic State strongholds in Raqqa and along the Euphrates River valley. The Trump administration's long-term strategy, following the defeat of the Islamic State, appears to be focused on stitching together a series of regional cease-fire deals among the U.S.-backed rebels, the Syrian government and Russia.
Some analysts said the decision to end the program was likely to empower more radical groups inside Syria and damage the credibility of the United States.
"We are falling into a Russian trap," said Charles Lister, a senior fellow at the Middle East Institute, who focuses on the Syrian resistance. "We are making the moderate resistance more and more vulnerable. . . . We are really cutting them off at the neck."
Others said it was recognition of Assad's entrenched position in Syria.
"It's probably a nod to reality," said Ilan Goldenberg, a former Obama administration official and director of the Middle East Security Program at the Center for a New American Security.
U.S. intelligence officials say battlefield gains by rebels in 2015 prompted Russia's direct military intervention on the side of the Assad regime. Some U.S. officials and their allies in the region urged President Barack Obama to respond by providing the rebels with advanced antiaircraft weapons so they could better defend themselves. But Obama balked, citing concerns about the United States getting pulled into a conflict with Russia.
Senior U.S. officials said that the covert program would be phased out over a period of months. It is also possible that some of the support could be redirected to other missions, such as fighting the Islamic State or making sure that the rebels can still defend themselves from attacks.
"This is a force that we can't afford to completely abandon," Goldenberg said. "If they are ending the aid to the rebels altogether, then that is a huge strategic mistake."
U.S. officials said the decision had the backing of Jordan, where some of the rebels were trained, and appeared to be part of a larger Trump administration strategy to focus on negotiating limited cease-fire deals with the Russians.
Earlier this month, five days into the first cease-fire in southwest Syria, Trump indicated that another agreement was under discussion with Moscow. "We are working on the second cease-fire in a very rough part of Syria," Trump said. "If we get that and a few more, all of a sudden we are going to have no bullets being fired in Syria."
One big potential risk of shutting down the CIA program is that the United States may lose its ability to block other countries, such as Turkey and Persian Gulf allies, from funneling more sophisticated weapons — including man-portable air-defense systems, or MANPADS — to anti-Assad rebels, including more radical groups.
Toward the end of the Obama administration, some officials advocated ending the CIA program, arguing that the rebels would be ineffective without a major escalation in U.S. support. But the program still had the support of a majority of top Obama advisers, who argued that the United States couldn't abandon its allies on the ground and give up on the moderate opposition because of the damage that it would do to U.S. standing in the region.
Even those who were skeptical about the program's long-term value, viewed it as a key bargaining chip that could be used to wring concessions from Moscow in negotiations over Syria's future.
"People began thinking about ending the program, but it was not something you'd do for free," said a former White House official. "To give [the program] away without getting anything in return would be foolish."