General Tony Thomas denied that the four-year-old operation was brought to an end as a way to placate Russia and earn its support for a ceasefire in southwestern Syria.
It was a "tough, tough decision" but "absolutely not a sop to the Russians," Thomas said at a forum in Aspen, Colorado.
"It was, I think, based on an assessment of the nature of the program, what we're trying to accomplish, the viability of it going forward."
Asked about Thomas's comments, the CIA declined to comment.
On Wednesday the Washington Post reported the covert CIA program was being shut down.
The Post said President Donald Trump made the decision nearly a month ago after a meeting with CIA chief Mike Pompeo and National Security Advisor HR McMaster.
The Post said Trump made the decision in a effort to find ways to work with Russia in Syria, where Moscow supports Assad's government.
Trump has said the main US focus in Syria should be to eliminate the Islamic State group, rather than opposing the Assad regime.
The ceasefire, which covers some of the area from which the rebels operate, was announced on July 7 at the G20 Summit in Hamburg, Germany.
President Barack Obama approved the rebel aid program in 2013 as various insurgent groups sought external support in a general uprising against the Assad regime.
Thousands of Syrian anti-government fighters were trained and armed.
But the US commitment remained ambiguous amid doubts in some quarters that the rebels could actually manage to depose Assad and as attention turned to the rising power of the Islamic State group in Syria and Iraq.
Support for the program further eroded last year after the rebels lost the areas they held in the Syrian city of Aleppo under a brutal Russian-backed government assault.
US officials said this week that some of the anti-Assad forces could be absorbed into US military-supported groups fighting Islamic State.
