Team spokesman Art Chase said both players had surgeries Sunday.
Jones fractured his left clavicle while taking a blindside hit during the third quarter Blue Devils' 21-7 victory at Northwestern on Saturday. Backup Quentin Harris played the fourth quarter at quarterback. Jones threw three touchdown passes before he was injured.
Gilbert injured his left hip in the second quarter.
Duke (2-0) plays at Baylor (2-0) on Saturday.
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