Nadal’s withdrawal comes just over three weeks before the U.S. Open gets under way at Flushing Meadows.
Djokovic, bidding for a fourth successive Wimbledon title and seventh in all, had earlier lost the opening set to Norrie following a rash of errors.
One time, the 27-year-old and world number 40, received a $10,000 fine for spitting in the direction of a spectator who had heckled him during a game.
World number one Iga Swiatek won her 36th consecutive match to record the longest winning streak in the women’s game in the 21st century.
“I tried to play as long as I could and I’m sorry I couldn’t give you any more.”