The hard-fought triumph over the former world number one from Serbia made Romania's 23-year-old Halep the first player to win three WTA titles this year.
Halep, ranked third in the world, won four of the final five games in the third set to earn the marathon victory in two hours, 37 minutes.
"I don't know how I won today because I didn't play my best," Halep said. "But I just wanted to fight till the end. Every match was very important for me, for my mind.
"I'm really happy that I have another title."
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Halep and Jankovic have a history of playing long, tight matches and Sunday was no different.
They have now gone to three sets in all five career meetings with Halep leading the series 4-1.
Jankovic, who served for the match at 5-4 in the second set but couldn't close it out, was gracious in defeat.
- 'Two dogs running' -
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"My opponent Simona was unbelievable," said Jankovic, who turned 30 last month. "She was running like two dogs, left and right for about three hours and at the end I just couldn't keep up anymore.