The all-Russian affair in eastern China was a battle of the two favourites, with top-seeded Medvedev - now the world number six - edging out his compatriot.
The first set followed serve until Rublev slipped up at 5-5, handing the initiative to his opponent.
The rattled world number 24 then lost serve again in the first game of the second set and was playing catch-up from then on.
The win rewarded a consistent performance from Medvedev, who savoured his first title since Dubai in February.
It was the 24th of his career on the tour.