The 30-year-old Serbian star had targeted Abu Dhabi for his first match since his quarter-finals loss at Wimbledon in July this year.
Djokovic was scheduled to play Spain's Roberto Bautista Agut in the semi-finals of the exhibition tournament at 1900 local time.
But four hours before that, Djokovic released a statement on his website announcing his intention. It is not clear still if he will play the Qatar Open where he is top seed next week.
"Unfortunately, in the past few days I started to feel pain in the elbow and after several tests, my medical team has advised me not to risk anything, to withdraw from the tournament and to immediately continue with the therapies."
More From This Section
He added: "Now I need to accept this situation, and to wait for the results of the therapies, in order to start playing tennis again and getting back to full rhythm. This might affect the start of the season and the tournament plan, but the decision will be made in the following days."
Murray also hasn't played a match since his loss at Wimbledon to Sam Querrey.
He had been suffering from a hip injury and was spotted in Abu Dhabi on Thursday practicing with his coaching team.
The second semi-final of the tournament is between world No 5 Dominic Thiem of Austria and world No 14 Kevin Anderson of South Africa.
On Saturday, prior to the men's final, former women's No 1 and 23-time Grand Slam champion Serena Williams will make her return to court with an exhibition match against the reigning French Open champion, Jelena Ostapenko.