The strike began in the early evening, when planes attacked a group of vehicles that American surveillance aircraft had been watching for several days, according to a Centcom official who requested anonymity because the episode was still being investigated. Military intelligence had identified the cluster of vehicles, which the official said included at least one tank, as belonging to the Islamic State, the official said.

The attack went on for about 20 minutes, with the planes destroying the vehicles and gunning down dozens of people in the open desert, the official said. Shortly after this, an urgent call came into the American military command center in Qatar, the outpost in the Persian Gulf that coordinates the aerial campaign in Syria and Iraq.

The call was from a Russian official who said that the American planes were bombing Syrian troops and that the strike should immediately be called off. The Centcom official said the attack was halted within minutes, but not until dozens had been killed.

Russian planes would most likely have been providing air support to government forces in the province during the fighting there. Russian warplanes had also been targeting the area where the government’s clashes with the Islamic State occurred, according to the Syrian Observatory for Human Rights, a monitoring group based in Britain.

Aaron David Miller, a Middle East analyst at the Wilson Center, said the episode was certain to make “an already complex situation more byzantine.”

He said the strikes would “feed conspiracy theories that Washington is in league with ISIS,” as well as create a pretext for Mr. Assad to avoid his commitments under the cease-fire deal. Mr. Miller added that the episode would create opportunities for President Vladimir V. Putin of Russia “to blast the U.S. on the eve of the U.N. General Assembly,” the global meeting in New York starting this week.

Samantha Power, the United States ambassador to the United Nations, accused Russia of pulling a “stunt” by calling for an emergency Security Council meeting over the episode.