It took Chung just under two hours to win his first ATP title, sealing the result with a powerful crosscourt forehand.
Chung, who was seeded sixth, didn’t lose a match all tournament, and had already beaten Rublev in straight sets in his second match in the round-robin group stage.
The South Korean was forced to come back from a set and a break down, however, in the final.
Chung wasted two match points on Rublev’s serve before clinching the title in his next service game.
It was South Korea’s first title since 2003.
The Next Gen Finals featured the top seven 21-and-under players in the rankings plus one Italian wild card.
The tournament also trialed new rules, including shortened sets, no-Ad scoring, shot clocks, Hawk-Eye line calls, and no lets on serve.