Osaka, 18, fought back from 5-0 down in the second set but world number 28 Wozniacki wrapped up her 24th career title in just under two hours.
The Dane, 26, has now won a tournament in every season since 2008.
"I'm enjoying it at the moment," said Wozniacki, who received treatment for a thigh injury during the final.
"Injuries happen and you never know when you can be taken out of the game, so I'm just savouring every minute."
Former world number one Caroline Wozniacki beat Japan's Naomi Osaka 7-5 6-3 to win the Pan Pacific Open in Tokyo for the second time.