The former world number one triumphed 3-6 7-6(4) 6-1 to claim her 15th WTA Title and second of the year.
The success came shortly after compatriot Novak Djokovic beat Jo-Wilfried Tsonga to win the Shanghai Masters title in China.
Kerber needed a win to secure a place in the eight woman end-of-season WTA Finals in Singapore next week and started brightly with an opening break as she took the set 6-3.
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The second proved another tight affair with three breaks of serve each before a tiebreak which Jankovic edged 7-4 after both players excelled with returns.
Jankovic was buoyed by the success and found her serving rhythm in the decider as Kerber failed to force a break point and collapsed as the Serb ran out a strong winner.
(Writing by Patrick Johnston in Singapore)
