The 22-year-old Russian, who returned to action in May after a right shoulder injury, won the battle between the former world number ones to regain the title she won in 2005, when the Serbian seventh seed retired with an arm injury at 5-2.
"It was very tough because Jelena started off so strong. It was my second final of the year, so I was a little bit nervous," said Sharapova.
"I wanted to perform really well. I feel like I played good enough tennis to give her a go today and I just wanted to keep fighting out there."
Sharapova found herself 0-40 down in the opening game, which she lost two points later, hitting a backhanded drop shot wide.
She then went 0-2 down before moving into top gear, hitting an array of power-packed strokes and aggressive service returns to take the following four games in a row.
Jankovic, who needed court-side treatment to her right arm in the semi-finals on Friday, took a medical time-out for the same injury at the beginning of the eighth game.
But Jankovic abandoned the match when she went down love-30.
"It's never easy to win a match like this. Obviously, it's very important for Jelena to be healthy and we want to compete at our 100 percent," said Sharapova.
"It's very difficult for her to perform at her best right now. We have gotten a lot of injuries. This is towards the end of the year. I wish Jelena a speedy recovery," added Sharapova.
It was Sharapova's fifth win against Jankovic in seven meetings, earning her the 350,000-doller top prize.
For Sharapova, who claimed her first career WTA singles and doubles titles at the 2003 Japan Open on the same court here, it was her first title since Amelia Island in April 2008, and 20th overall, four of them won in Tokyo.