Chung, 21, was outplayed in the first set and was 3-1 behind in the second set before taking over to win 3-4(5) 4-3(2) 4-2 4-2 to go through the five-day round-robin tournament unbeaten.
A high-quality final full of sublime ball-striking was a fitting end to a promising debut for an event which has experimented with a range of innovations such as shorts sets, 'sudden-death' deuces and on-court coaching.
The 20-year-old Rublev, at 37th the highest-ranked qualifier for the event restricted to players aged 21 and under, lost his cool as the relentless Chung turned the match around.
But the Muscovite showed tremendous resolve to survive a deciding point deuce, effectively match point, when serving at 1-3 in the fourth set, winning a ferocious baseline exchange.
The 54th-ranked Chung showed his first sign of nerves when he double-faulted at 30-30 in the next game but Rublev wasted the break point with a shanked forehand.
At deuce Rublev still had the chance to drag the set into a tiebreak but Chung struck a forehand winner to seal victory in just under two hours of compelling action.
Chung, 21, is the first South Korean to win an ATP singles trophy since Hyung Taik-lee captured the 2003 Sydney title by beating Juan Carlos Ferrero.
Rublev, who began his ATP Tour title collection in Umag this year, looked close to tears at the end but his performance, and that of Chung's, suggested both will be challenging for some of the biggest prizes in the sport before long.
Add in the likes of Canadian teenager Denis Shapovalov, who dazzled in the Fiera Milano venue earlier in the week, beaten semi-finalists Daniil Medvedev and Croatian Borna Coric and a third Russian, Karen Khachanov, not to mention American Jared Donaldson, and the future looks bright for the men's Tour.
Whether or not any of the rule changes trialled this week ever become regular features remains to be seen, although the 25-second shot clock and shorter warm-ups were popular with players and fans alike.
(Reporting by Martyn Herman, editing by Pritha Sarkar)
