The pair had been scheduled to face each other for a 37th time in their careers in what was a first since meeting in Doha back in 2017.
But a little over an hour before the pair were due on court in the last-16 encounter at the Madrid Open, tournament organisers announced the late withdrawal of Murray in the opening match on Manolo Santana Stadium.
In a brief statement, it said: “Unfortunately, Andy Murray is unable to take to the Manolo Stadium due to illness. We wish you a speedy recovery.”
Instead, Murray’s fellow Briton Dan Evans was brought in for the first match on the main show court against No6 seed Andrey Rublev, with the pair having previously been scheduled to play inside the Aranxta Sanchez Stadium.
Murray had enjoyed an impressive run of form in his first set of matches on clay since 2017. He had set up the meeting with world No1 Djokovic after knocking out Denis Shapovalov in three sets having previously beaten another former top-10 player in Dominic Thiem in the preceding round in the Spanish capital.
There had been no signs of sickness from the 34-year-old Murray after coming off court late on Tuesday with the Briton insisting he hoped to use the match as a benchmark for his form and fitness.
“He’s No1 in the world and I’m playing with a metal hip so I shouldn’t have a chance,” he said. “It’s a great opportunity for me to see where my game’s at.”