The match was all square at 7-5, 6-7, 2-2 when the world number 67 called an end to the contest at the Qizhong arena because of what appeared to be a right wrist injury.
Gonzalez, the world number 12, secured the first set with a superb backhand but mixed sublime shots with a string of feckless errors as the German's aggressive tactics paid off.
"It was a really weird match. I felt the match almost in my hand in the second set and then it was turned over," Gonzalez told reporters.
"I don't feel my best now, but I'm glad that I keep winning. I try my best, but sometimes you don't find the way that you really want to be. Maybe I'm tired?"
The 22-year-old Zverev first got treatment on his hand after a fall in the opening game of the third set and decided he could not continue three games later.
Chilean Gonzalez, one of a handful of players competing for the last three spots at the season-ending World Tour Finals, will next play Brazilian qualifier Thomaz Bellucci.
ACE ONSLAUGHT
American James Blake earlier set up a second meeting in a week with top seed Rafa Nadal by standing his ground against an onslaught of 27 aces from Croatian Ivo Karlovic to win their first-round match 3-6, 7-6, 6-3.
Blake lost an entertaining match against the world number two in Beijing last week and was under no misapprehensions about what he faces in the second round in China's financial capital.
"I know how difficult it is to play him," the New Yorker told reporters.
"I know how much he makes you run, how hard he makes you work, how great defense he plays.
"I know what I'm in for, and I'll just prepare same way I did last week, just make sure my legs are fresh and be ready to face one of the best in the world."
Qualifier Lukasz Kubot spurned a chance to reacquaint himself with Andy Roddick, who he beat at the China Open last week.
Swiss Stanislas Wawrinka came from behind to beat the Pole 2-6, 7-6, 7-6 in a three-hour match and will play the American fourth seed in the second round.
Former world number one Marat Safin, who beat Gonzalez last week in Beijing, continued his march towards retirement with a 6-4, 6-4 victory over Chinese wildcard Gong Maoxin.
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