Ahmadreza Afshari of the IRGC's "aerospace advisory forces" in Syria was "martyred because of injuries caused by aerial bombardment", Guards' chief Hossein Salami said in a statement carried by state news agency IRNA.
The colonel was transferred from Syria to Iran for treatment following the air strike, the statement said, indicating the incident occurred two to three weeks ago.
In late July, the Syrian Observatory for Human Rights war monitor said an air strike killed three pro-Iran fighters in Syria's Deir Ezzor province, where Iran wields significant influence.
The area is regularly targeted by Israel and sometimes by the United States.
Responsibility for the strike was not immediately claimed.
A spokesman for the US-led military coalition formed in 2014 to fight the Islamic State jihadist group said at the time that "neither the coalition nor US forces carried out overnight strikes in Deir Ezzor".
Since the beginning of the Syrian civil war in 2011, Israel has carried out hundreds of strikes mainly targeting army positions and Iran-backed fighters, including from Lebanon's Hezbollah group.
Israel rarely comments on individual strikes in Syria, a key ally of the Islamic republic.
Regional tensions, already heightened by the Israel-Hamas war in Gaza, intensified further following the July 31 killing of Hamas political chief Ismail Haniyeh during a visit to Tehran.
Iran blamed Israel for the death of Haniyeh and vowed to avenge it.
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