Judiciary spokesman Alireza Jamshidi said the stoning was carried out near the town of Takestan, in the northwestern province of Qazvin.
The Stop Stoning Forever campaign in Iran earlier said Jafar Keyiani's execution occurred on July 5.
The execution was condemned by several prominent rights defenders, including Iranian Nobel Peace Prize winner Shirin Ebadi.
"I'm very regretful that the stoning sentence was carried out because this sentence is not in line with Iran's international commitment and also [the head of Iran's judiciary] has issued several rulings that stoning sentences should not be carried out," Ebadi told Radio Farda.
United Nations Human Rights Commissioner Louise Arbour also condemned the stoning, and urged Tehran to spare the victim's partner -- who reportedly was jailed at the same time 11 years ago -- the same fate.
Under Iranian law, adultery is still punishable by stoning, although the judiciary issued a directive suspending the practice in 2002.
(with AFP, dpa, IRNA, ISNA)