Kontaveit won her fourth title in the past 10 weeks and fifth overall with a 6-2 6-3 victory over former world No.1 Simona Halep.
The second-seeded Kontaveit didn't drop a set in the tournament while winning her second straight title, after victory at the Kremlin Cup in Moscow last week.
Her strong finish to the season with 26 wins from her past 28 matches sealed the eighth and final place at the WTA Finals in Guadalajara, Mexico.
She is the first player from Estonia to qualify for the elite event.
Kontaveit will also enter the top 10 for the first time when the rankings are updated Monday.
She had not won a set in three previous meetings with Halep, but denied the home crowd favourite a 23rd career title on Sunday.
Kontaveit lost serve at 5-1 but broke back right away to take the opener.
"I'm still unsure of what's going on!" Kontaveit said.
"Of course, I'm incredibly happy that I managed to play really well today and win the final.
"That was the main focus and I'm really, really proud of myself that I managed to do that."
Top-seeded Halep started the second set with an early break to go 2-0 up, but lost the next five games, as Kontaveit wrapped up the win on her fourth match point.
"She deserved definitely to win the match," Halep said.
"I just tried to make it longer a little bit, but I couldn't.
"But many positives this week: to play a final after a tough year, it's always welcome."
Halep - who missed Roland Garros, Wimbledon and the Tokyo Olympics due to a calf injury - extend her streak two 12 years of playing in a WTA tour final.
Meanwhile, Donna Vekic won her first title for four years, beating Denmark's Clara Tauson in two sets in the Courmayeur Ladies Open final in Italy.
Croatian Vekic, who had knee surgery in February, won 7-6 (7-3) 6-2 in less than an hour and did not drop a set all week.
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