Ghassem Hassanzadeh, an IRGC official, told the official state daily “Iran” that the clashes took place in the province of Sistan-va-Baluchistan late on Thursday.
He said that a further nine members of the IRGC and its affiliated para-military Bassij force were also wounded in the incident.
He accused the rebels of drug trafficking.
Iranian authorities routinely execute dissidents on bogus charges such as armed robbery and drug smuggling.
State television reported on Friday that four rebels had been killed in clashes with the IRGC near the provincial capital of Zahedan.