The Serb added to previous successes in Auckland, Monterrey and Birmingham with a 6-2 7-6 (7-2) win in one hour and 39 minutes in Saturday's Tokyo final.
Ivanovic lost the 2007 showpiece at the same WTA international hard court event but she broke through on this occasion, making it her most successful year on tour.
Wozniacki " runner-up at the US Open earlier this month " was seeking her second win at the tournament but was again defeated in a final.
The third seed started in superb fashion, breaking Wozniacki at the first opportunity.
But despite Ivanovic consolidating her break to lead 2-0, Wozniacki quickly levelled at 2-2.
Then came a lengthy game of 17 points, Ivanovic claiming the break straight back with her third chance.
Ivanovic hit 19 winners in the opener and had great success in coming to the net, successful on eight of 11 attempts, as she won the last four games of the first set.
Wozniacki, seeded second, fought back strongly, moving into a 3-1 lead, but a run of four successive breaks robbed her of momentum.
And after taking the second set to a tie-break, Ivanovic won the last six points to continue her excellent year.