The world number one was beaten 6-2 6-7 (4-7) 6-0 by the Russian second seed, who drove a forehand past Djokovic on his third championship point.
Djokovic was seeking a third triumph at this tournament, and an 87th tour-level title of his career, but 24-year-old Rublev came out on top, scooping his third trophy of the year after previous successes in Dubai and Marseille.
Having been barred from playing in Australia and the United States in the early stages of the season, due to being unvaccinated against COVID-19, Djokovic was playing just his third tournament of the year.
He lost to Jiri Vesely in the Dubai quarter-finals and to Alejandro Davidovich Fokina in his clay campaign opener in Monte Carlo, and on home clay he won three matches from a set in arrears but could not make it four in a row.
Djokovic had worked hard to get back on level terms in Sunday’s final after making a slow start, and he had two break points immediately in the third set.
Rublev saved both, the second with an audacious drop shot, on his way to taking the game, and he streaked through the rest of the decider.
This was just the second meeting on the ATP Tour between Djokovic and world number eight Rublev, with Djokovic having previously enjoyed a crushing hard court win at the ATP Finals in Turin last November.
Rublev, addressing Djokovic, said: “It’s a big honour to play against you, to share a court for the second time.
“I hope to see you for many years, and we will have more battles which I would like.
“I feel so great here in Belgrade. It’s a really nice city. It reminds me of a small Moscow. I really enjoy my time here and to win a title here I feel double special.”
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