The official said al-Muhajir was in northwest Syria at the time of the strike, but that he usually operated in the east.
It was not immediately clear how the U.S. military confirmed that the person killed was al-Muhajir; no other details were provided.
In a statement Sunday, U.S. Central Command said there are no indications any civilians were killed in the strike. The military was assessing reports a civilian may have been injured.
Friday was the third day in a row that U.S. officials complained that Russian fighter jets in the region had conducted unsafe and harassing flights around American drones.
Lt. Gen. Alex Grynkewich, head of U.S. Air Forces Central Command, said in a statement that during the Friday encounter, the Russian planes “flew 18 unprofessional close passes that caused the MQ-9s to react to avoid unsafe situations.”
The first friction occurred Wednesday morning when Russian military aircraft “engaged in unsafe and unprofessional behavior” as three American MQ-9 drones were conducting a mission against IS, the U.S. military said. On Thursday, the U.S. military said Russian fighter aircraft flew “incredibly unsafe and unprofessionally” against both French and U.S. aircraft over Syria.
Col. Michael Andrews, Air Forces Central Command spokesman, said the Thursday incident lasted almost an hour and included close fly-bys, by one SU-34 and one SU-35 and that they deployed flares directly into the MQ-9.
U.S. officials said the drones were unarmed in the earlier flights, but were carrying weapons on Friday, as they were hunting al-Muhajir.
“We have made it clear that we remain committed to the defeat of ISIS throughout the region,” said Gen. Erik Kurilla, commander of U.S. Central Command, in the statement.
Rear Adm. Oleg Gurinov, head of the Russian Reconciliation Center for Syria, said this past week that the Russian and Syrian militaries had started a six-day joint training that ends Monday.
Gurinov added in comments carried by Syrian state media that Moscow was concerned about the flights of drones by the U.S.-led coalition over northern Syria, calling them “systematic violations of protocols” designed to avoid clashes between the two militaries.