Second-seeded Djokovic, 32, defeated fifth-seeded Thiem, 26, with a score 6-4, 4-6, 2-6, 6-3, 6-4. The match, held in Melbourne, lasted almost 4 hours.
This is the 17th Grand Slam title for Djokovic, who won the Australian Open for the second consecutive year.
On Monday, Djokovic will take over Spain's Rafael Nadal to lead the Association of Tennis Professionals rankings. Nadal lost to Thiem in the tournament's quarterfinal.