The 15th-seeded Swiss had taken a 6-1 5-2 lead over the world number one with a powerful serve and booming groundstrokes before Djokovic took greater control of the rallies and waited for Wawrinka to make mistakes.
Wawrinka, however, managed to send the fourth-round match into a decider when he totally dominated the fourth set tiebreak before Djokovic clinched a tense 1-6 7-5 6-4 6-7 12-10 victory on his third match point in five hours two minutes.
Djokovic, seeking to become the first man in the professional era to win three successive Australian Open titles, will now meet fifth seed Tomas Berdych in the quarter-finals after the Czech overcame South Africa's Kevin Anderson.
(Reporting by Greg Stutchbury; Editing by John Mehaffey)
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