The two men ran for the vice presidency last May, with Cayetano as Duterte's running mate. The Marcos family, meanwhile, remain Duterte's staunch allies.
Candidates who lose in elections are banned from taking appointive positions in government for a year.
In a television interview, Duterte said Cayetano will take over the post of Foreign Affairs Secretary Perfecto Yasay, who is going back to the United States to fulfill his obligations as a professor of international law.
"Alan would be coming in to take his post," Duterte said, keeping to his word during the campaign.
President Duterte also revealed that Marcos was interested in the Department of Tourism post.