"Several rebels" also died in the Thursday night fighting, ISNA quoted a military official as saying, adding that a car and weapons were seized.
The clashes erupted in Iran's restive province of Sistan-Baluchistan, where attacks by rebels earlier this month killed five people, four of them security forces.
Iranian media said 14 people were arrested in connection with those attacks.
Last month an Iranian soldier was killed and two pro-government militiamen wounded in an attack blamed on the Sunni extremist group Jaish-ul Adl (Army of Justice).
Sistan-Baluchistan province has a large Sunni Muslim community in an otherwise predominantly Shiite country, and has been plagued by violence involving Sunni extremists and drug smugglers.
Iran has repeatedly asked Pakistan to act to "stop the infiltration of terrorists" and has tasked the elite Revolutionary Guards to monitor the restive border region.