The Australian No.1 had progressed from his semi-final after Poland's Hubert Hurkacz retired injured when trailing in the second set.
Djokovic was leading 7-5 5-3 in Beijing and serving for the match when the incident happened.
After a forehand volley winner from Djokovic, the ball bounced off the advertising boards toward Medvedev, who smacked a backhand that sailed into the stands.
It hit a spectator in the front row behind him. He clutched his left eye and appeared to be in pain as he walked out, assisted by stadium staff.
"Terribly sorry to the spectator, first of all," Medvedev told reporters." I'm trying to get in touch with him, if he wants it. Hopefully I can apologise in person and see how he feels."
The Russian world No.5 said he did not cause the incident intentionally.
"The ball was bouncing back, so I tried to, like, just hit it anywhere, so it doesn't go out from the court. When I saw the result, I mean, I felt horrible because, again, I don't think I was ever close to such a situation."
Medvedev, 30, has a history of on-court behaviour issues. He was fined 6,000 euros ($A9,600) after he smashed his racquet seven times during a 6-0 6-0 loss to Matteo Berrettini at this year's Monte Carlo Masters.
"I was shocked, to be honest... I hope that person is not badly injured," said Djokovic, who was disqualified from the US Open in 2020 under similar circumstances.
"On the other hand, I also feel sorry for Daniil because I know exactly how it feels to be disqualified in a big match ... I'm sure that Daniil didn't want to do this intentionally."
De Minaur will be seeking to become the first person to beat Djokovic in 34 matches at the China Open. He has a 1-3 head-to-head record with the Serb.
The winner will leave Beijing ninth in the race to qualify for November's eight-man ATP Finals with the gap to Medvedev in eighth reduced as the Russian will lose the 200 points he had gained in Beijing.
There are two ATP Masters 1000 events to come, in Shanghai and Paris, but ninth may be enough with Jannik Sinner's availability uncertain.
On Saturday the world No.1, who last played at Wimbledon, pulled out of Shanghai, which begins on Wednesday. The Italian has a knee problem.
De Minaur was up 6-4 3-2 and 40-0 when Hurkacz retired with an apparent adductor injury after showing mobility problems.
The world No.9 had broken a tentative Hurkacz in his opening two service games before holding to lead 4-0, then withstood a comeback to take the first set 6-4.
Another break in the third game of the second set helped de Minaur build a 3-1 lead. Hurkacz fought desperately to hold serve in the following game - surviving four break points and a marathon deuce game - but was unable to battle much longer.
In Tokyo, defending champion Carlos Alcaraz overcame early wobbles on his serve to outclass fellow Spaniard Jaume Munar 5-7 6-3 6-1 and reach the Japan Open final.
The 23-year-old was a break up 5-4 in Tokyo before gifting the opening set with two shaky service games.
After a sluggish start to the next set - completing a run of 16 straight losing points - Alcaraz raised his level to set up a final with Jiri Lehecka, who beat Valentin Vacherot 6-4 6-2.
with agencies
