Djokovic was up 6-4, 6-4, 2-0 when Djere pulled the plug on a gritty encounter that saw both men summon the physio to Arthur Ashe Stadium.
"It's not what we want to see," Djokovic said. "He's such a good player in these conditions and the second set should have been his, he was 4-2 up.
"I don't know if (my) winning the second set probably put more burden on him."
Djokovic notched his goth US Open match victory, becoming the first man to win go at all four Grand Slams.
But it was a battle until the minute Djere called it quits.
Djokovic grabbed the first break of the match to take the first set 6-4 after a tense hour then sought treatment for trouble on his right side.
Djere, the only player to take a set off Djokovic at last year's US Open, gained the first break of the second set and with a 4-2 lead had two more break points that he couldn't convert.
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