Maj. Gen. Ataollah Salehi said Iran "will not repeat its warning" to the vessel and the country would respond to threats, Iran's official Islamic Republic News Agency reported.
An Iranian warplane identified the U.S. ship as it patrolled the area of naval drills, officials said.
Salehi said the naval drills, which ended Monday, were designed to maintain the country's military strength to ensure the nation's interests were safeguarded. The 10 days of drills began in the Strait of Hormuz.
Rear Adm. Mahmoud Mousavi, a deputy naval commander, told IRNA naval forces targeted hypothetical enemies and successfully destroyed them.
Mousavi also said three super-modern missiles -- Qader, Nasr and Nour -- were tested successfully.