The former top-ranked player from Serbia dictated from the baseline throughout the 1½-hour match, hitting the lines and keeping Wozniacki on the run.
Jankovic broke Wozniacki three times in the first set and again in the first game of the second set.
"I wanted to be really aggressive, but at the same time patient, and not really go for too much or go over the limit with some balls," Jankovic said. "I waited for my opportunities, and when I had them, I took them."
Wozniacki brought her coach, who is her father, on court once in each set, but it didn't help. She never found a solution to Jankovic's pinpoint power.
"I tried to change it when I saw it was not going my way, but I just made a few too many errors at the important points," Wozniacki said.
She held to trail 5-4 in the second set, prompting Jankovic to summon her coach. Jankovic then served out the match, setting up match point with a backhand down the line. Wozniacki's forehand return sailed long on the final point.
"I was making a few too many errors and I didn't have too many first serves in," said Wozniacki, who won 19 of 30 first-serve points. "Normally, the other matches I set the points up with my service well. That didn't happen today. Then I was on the back foot and she was deciding."
Jankovic kissed her racket and later did the same to the crystal trophy, which was so heavy she couldn't lift it in triumph.
"I haven't been working out in the gym lately," she said. "Caroline could have done a better job. She should have helped."
Two years removed from being the world's No. 1 player, Jankovic is projected to rise to No. 8 when the WTA Tour rankings are released Monday. She hadn't won a title since August at Cincinnati; Indian Wells is her 12th career title.
"I'm looking to playing some good tennis and really doing the right things out there," she said, "and if I'm doing that, I'll be winning big titles and the ranking will come on its own. I'm looking to do well in the big events.
Wozniacki, last year's U.S. Open finalist, has yet to beat Jankovic in four meetings. The 19-year-old Dane will reach a career-high No. 2.
She had her best year yet in 2009, reaching eight finals and winning three. She lost to Kim Clijsters in her first Grand Slam final at the U.S. Open.
Information from The Associated Press was used in this report.