"I am terribly disappointed that I am forced to withdraw from the Mubadala World Tennis Championship," Djokovic said in a statement.
"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.
"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."
Djokovic was released at the event in Abu Dhabi by Andy Murray, who was also on his way back from injury.
The match against Bautista Agut was Murray's first in six months as, like Djokovic, he hn't played since his quarterfinal-exit at Wimbledon.
The Scotsman was handed a heavy 6-2 defeat in the AAbu Dhabi exhibition, but said he felt better as the match progressed.
"Obviously a bit slow at the start," he told the Telegraph. "Roberto is one of the best players in the world and when you haven't competed for a long while it takes time to get back up to that pace. I started to feel a bit better towards the end, but I'll need to keep improving for sure."
Murray will now travel to Brisbane for a warm-up tournament before the beginning of the Australian Open on January 15.
