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United, still beset by injuries to their first-choice back four, fielded a makeshift defence featuring midfielders Michael Carrick and Darren Fletcher, as well as youngster Ritchie de Laet.
Seconds into the second half, Fulham were 2-0 up after Zamora lashed in a half-volley following a knockdown from Clint Dempsey.
Zamora then set up Duff, who volleyed home 15 minutes from time.
Arsenal are two points behind United in third after Brazilian midfielder Denilson's delightful free kick set them on the way to a 3-0 victory over Hull City.
They had to survive a Geovanni missed penalty after the break before adding two more goals through Eduardo da Silva and Abou Diaby.