Serb Djokovic had dismissed Stan Wawrinka in the semi-finals of the exhibition event on Friday but the defending champion revealed on Saturday he was suffering from a fever.
Murray had himself complained of pain in his left shoulder during his 6-2, 6-0 win over Rafael Nadal in the last four.
The Scot is set to undergo a scan before continuing his build-up to the first Grand Slam of the season, the Australian Open, at the Hopman Cup in Perth next week.
Murray will join Heather Watson to represent Britain at the mixed team event, with their opening match due to be against France on Monday. -AFP