There is no timetable for his return.
"We feel very badly for Ryan," Duke coach Mike Krzyzewski said. "He is playing the best basketball of his career and this is a tough setback for him. We're hoping for a good recovery and we are optimistic about his return."
Kelly had 12 points in the first half against Clemson but sat out the second. Krzyzewski said Kelly hurt the same foot he tweaked during the holidays and sprained last March, an injury that kept him out of both the ACC and NCAA tournaments.
Kelly is averaging 13.4 points, 5.4 rebounds and 1.7 blocks per game for the season. He had scored in double figures in 13 of Duke's 15 games.
Kelly ranks third all time in career winning percentage (105-13, .890) for the Blue Devils.
Duke visits No. 20 North Carolina State on Saturday.
Information from The Associated Press was used in this report.