The full details of what was behind the 15-member panel's decision to effectively sack Yasay were not immediately clear. Yasay is a member of Duterte's inner circle.
Numerous allegations have been made against Yasay, a U.S.-educated lawyer, including that he illegally held U.S. citizenship when he was appointed foreign affairs secretary.
Lawmakers in his earlier hearing had pointed to inconsistencies in statements he made before the congressional committee and in media interviews this week, about whether he had been a U.S. citizen, had held an American passport and the status of applications he had previously made to be naturalized.
Yasay was not present for the decision and an aide who answered his cellphone said there would be no immediate statement from the former minister.
Panfilo Lacson, chairman of the Senate foreign affairs committee, said the Commission on Appointments was unhappy with Yasay's conflicting comments under oath, and their decision was final.
"We all know how close attorney Yasay is to the president. It was the view ... that he was not telling the truth, he was not forthright in the question-and-answer portion of the hearings," Lacson told reporters.
Philippine Cabinet ministers must undergo a confirmation hearing, but these often take place long after they begin work.
Lacson said the decision proved that the commission was not just a rubber stamp.
Foreign affairs spokesman Charles Jose said in a text message the ministry respected the panel's decision and would ensure a smooth transition as soon as Duterte appointed a new foreign secretary.
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