Defending champion Jin was playing catch-up since Choi unexpectedly dominated qualification and entered the final with a seven-point lead over his favoured teammate.
Jin closed in at almost every round, before ultimately topping Choi by 0.5 point to earn his second gold medal in London after winning the 10-meter air pistol event last Saturday.
"It's a great pleasure for me, but Choi expected the gold so I feel sorry to have taken it away from him," said Jin, adding that the two were planning to have dinner together to celebrate their achievements.
"I didn't expect to win this gold," said Jin, who only qualified in 5th position for the final. "I was hoping for bronze. After the fifth shot, I didn't look at the scores anymore."
Jin beat Choi 662-661.5 points, while Wang Zhiwei of China took bronze with 658.6 points after edging Xuan Vinh Hoang of Vietnam by the smallest possible margin of 0.1. Except for Jin, most favourites failed to qualify for one of the eight spots in the final.
The 22-year-old Choi, ranked 55th in the world, won silver in his first international shooting final. He is yet to reach the top ten of a World Cup event.
"I am so happy," he said, while repeatedly kissing his medal. "I did not expect this kind of performance. I just tried to stay in a good mindset and relax."
Choi said he did not follow the scores from his fifth to ninth shot to avoid getting nervous.
"Before my last shot, I just thought, I try my best and than I am fine," said Choi, adding he would "never" be disappointed with silver, even if gold had been so close.
Several medal hopes failed to advance from the qualification stage, most notably Tomoyuki Matsuda of Japan. The world champion shot 559 to share eighth place, then finished fourth in the six-man shoot-off for one remaining final spot.
Matsuda, who won four of the last 15 World Cup events he competed in, also missed out on the final of the 10-meter air pistol last Saturday.
Vladimir Isakov of Russia, who won bronze in Beijing four years ago, became another casualty in the shoot-off, which send Giuseppe Giordano of Italy through to the final.
World's No. 1 Damir Mikec of Serbia scored 558, one point short for the shoot-off and two for immediate qualification.