Yoon, speaking with South Korean troops stationed in Abu Dhabi early this week, said South Korea and the UAE are under "very similar" circumstances, each facing North Korea and Iran as "the enemy, biggest threat."
His remarks prompted a rare spat between Seoul and Tehran, at a time when relations have already been testy over frozen Iranian funds in South Korea and suspected arms dealings between Iran and North Korea.
Iran's deputy foreign minister on legal affairs, Reza Najafi, summoned Yun Kang-hyeon, the South Korean ambassador on Wednesday to protest against Yoon's "interventionist remarks," the official IRNA news agency said.
Najafi also accused South Korea of pursuing an "unfriendly approach" toward Iran, singling out its frozen funds.
Iran has repeatedly demanded the release of some $7 billion of its funds frozen in South Korean banks under U.S. sanctions.