Djokovic next plays Stanislas Wawrinka, who stayed in contention for one of the two remaining ATP finals spots by defeating Nicolas Almagro of Spain 6-3, 6-2.
Defending champion David Ferrer also advanced, eliminating Gilles Simon of France 6-2, 6-3.
Isner saved six break points to force the tiebreaker and took the first set when Djokovic's backhand sailed wide.
The second-seeded Serb raised his game in the second set, making only two unforced errors and breaking Isner twice. Djokovic then won the last five games of the match, finishing off Isner with a backhand volley.
Wawrinka, seeded seventh, rallied from a 3-1 deficit in the first set and broke Almagro twice in the second.
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