But there was no stopping the Serb once he made it on to Court One as he romped to a 6-4 6-2 6-2 win to reach the quarter-finals for a 10th time.
With Kevin Anderson taking almost 3-1/2 hours to tame French showman Gael Monfils in the previous match, Djokovic knew he had about two hours of daylight left if he wanted to avoid coming back on Tuesday's rest day to finish off the contest.
The 12th seed timed the conclusion almost to perfection, sealing victory at 8.50pm on his third match point after Khachanov dumped a tired backhand into the net to end a 20-stroke rally.
Djokovic, winner of three singles titles at the All England Club, will next meet Japan's 24th seed Kei Nishikori.
(Reporting by Pritha Sarkar; Editing by Ken Ferris)
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