Yasay had been appointed by President Rodrigo Duterte, who assumed office June 30, and previously denied that he had a passport from the United States.
The unanimous vote by the Commission on Appointment on Wednesday came after two confirmation hearings that centered on questions about his citizenship.
Yasay apologized to the body’s committee on foreign affairs, admitting he may have "inadvertently misled" its members.
"I am a Filipino and I am not an American citizen," he insisted.
Occidental Mindoro Representative Josephine Ramirez-Sato, a Commission member, said Yasay had U.S. citizenship, and requested its withdrawal last June when the Duterte administration took office.
The Philippine Star reported that the U.S. confirmed the request in February.