After Wawrinka moved to within one game from taking the match at 5-2, the Serb called for another time-out.
Again the delay helped Djokovic as he returned to hold serve for 5-3, but Wawrinka maintained his nerve to serve out the match and claim his third grand slam title.
In commentary for ESPN, brothers John and Patrick McEnroe criticised Djokovic's tactics. "Complete abuse of the rules," Patrick said. "(It's) up to the officials to do something about it, but they don't have the guts."
The pair joked that under the rules Djokovic could take a separate time-out for each of his toes and "then there's fingers".
Djokovic revealed during the trophy ceremony he was unsure whether he was even going to enter the tournament because he was "struggling physically".
Wawrinka wore Djokovic down to beat the defending champion 6-7 (1-7) 6-4 7-5 6-3 for his first US Open men's title and third grand slam trophy overall.
The 31-year-old Wawrinka is the oldest US Open men's champion since Ken Rosewall was 35 in 1970.
Wawrinka has won only five of 24 career meetings against Djokovic, but has now beaten the 12-time major champion on the way to each of his own grand slam titles, including in the 2014 Australian Open quarter-finals and 2015 French Open final.
Before this matchup, Djokovic praised Wawrinka as "a big-match player," and, boy, is he ever. He wasn't always.
Playing in the shadow of his far-more-accomplished Swiss countryman and good pal, Roger Federer, Wawrinka needed until his 35th appearance at a major, at age 28, just to get to the semi-finals for the first time.
But look at Wawrinka now. He has now won 11 tournament finals in a row. He is 3-0 in grand slam finals, beating the No.1-ranked player each time.
And he did it against Djokovic, whose French Open title in June completed a career grand slam and made him only the third man - and first in nearly a half-century - to win four consecutive major tournaments.
- with AP