That came just days after Ali Shamkhani, secretary of Iran's Supreme National Security Council, visited Kabul and told reporters that talks had been held with the Taliban in Afghanistan.
The meeting signals Iran's role as a regional mediator to ease out tensions between the Taliban and Kabul.
Before this, the Iranian media said early this week that Tehran had hosted a Taliban delegation.
"A delegation of Taliban were in Tehran on Sunday and lengthy negotiations were held with Iran's Deputy Foreign Minister Abbas Araghchi," said Foreign Ministry Spokesman Bahram Ghasemi at a televised news conference.
The delegation was on a three-day visit to Iran.
The delegation has been led by Sayed Taib Agha and Mohammad Ullah Nomanee, the Taliban representatives in Qatar and Shamsuddin Pahlawan respectively. The former Taliban Governor of the Maidan Wardak province was also among the delegation.
The development happened at a time when the Afghan Foreign Affairs Ministry had said that discussions have begun over the credibility of Taliban's trip to Iran. On the other hand, a Taliban official confirmed the trip.
The Ministry stressed that Iran strongly supports Afghanistan's peace process.
"The position of Iran in connection with Afghanistan's peace process is clear and Iran will support the Afghan Government in its peace process," the Foreign Affairs Ministry Spokesman Janan Mosazai said.
MNA/PR