The former world number one, who would have regained top spot by winning the title, was down 7-6 (7-2) 2-0 when he withdrew with an elbow injury.
Djokovic, 30, had treatment on a right shoulder injury during his last-16 win over Adrian Mannarino and needed further attention against Berdych.
The Serb said he would consider whether surgery was needed to fix the injury.
"I haven't felt this much pain since I've had this injury," said Djokovic.
"It's not the shoulder, it's the elbow that has kept bothering me for over a year and a half.
"I was able, for 30 minutes, to play with some pain that was bearable, but the serve and forehand were shots where I could feel it the most. After that, there was really no sense [in continuing]."
