The Russian, dumped out of the US Open in the third round earlier this month, struggled from the start against a player 131 places below her in the world rankings.
"It's not an easy moment," Safina said after surrendering her Tokyo title.
"I had a lot of chances in the third set but I just let it go."
"The way I played the game at 5-4 was not right. It's so disappointing I didn't play the way I should have played. I never took her out of her comfort zone," Safina added.
Safina's ownership of the number one spot has been a source of contention after her failure to win a maiden grand slam in 2009 and the Russian got off to a bad start here by losing the first set tiebreak 7-5.
The defending Tokyo champion, given a first-round bye at the $2 million tournament, rallied to take the second with a thumping backhand.
But after seizing an early break in the deciding set, Safina's nervousness resurfaced as she tamely surrendered her serve with a double-fault at 5-4 up.
While Safina yelled at herself in Russian, the 18-year-old Chang kept her cool, completing the biggest win of her career by forcing Safina into wild forehand on her third match point.
"I never came into the match thinking I was going to lose badly. I just wanted to play tough," said Chang after winning a marathon match in two hours and 44 minutes.
"I was jumping up and down at the end thinking about my mum. She never watches me play but she watches the live scores so I was wondering what she was thinking."
Earlier, Ai Sugiyama's final WTA Tour appearance ended prematurely when the Japanese player retired from her first-round match with Russian Nadia Petrova while trailing 6-0, 2-1.