The loss ended an outstanding run through the tournament by Li, who became the first Chinese player to reach a Grand Slam singles final.
Li appeared to become upset with some of the Chinese spectators in the crowd in the third set and asked the chair umpire to intervene. She later complained about the flashes from photographers at center court.
However, Clijsters kept her composure all night.
The win for the reigning U.S. Open champion came in what could be her last appearance at Melbourne Park -- she had said 2011 might be her last full year on the tour.
After the match, though, she appeared to qualify that statement. She may go with a restricted schedule for 2012, when she wants to compete in the London Olympics.
"Yes, I hope so," she said when asked if she would be back to defend her title next year.
Clijsters, who has three U.S. Open titles, lost the 2004 Australian Open final to Justine Henin and has reached the semifinals here four other times.
"I finally feel like you guys can call me Aussie Kim because I won the title," said Clijsters during the trophy presentations, referring to her popularity after dating Australian star Lleyton Hewitt. "Even when things weren't going good, you guys were really supportive of me and I really appreciate it."
Looking at Li, Clijsters said: "I think we'll have a lot more tough battles to come. Hopefully, a few more Grand Slam finals would be nice."
Li, with her courtside humor and bubbly personality, endeared herself to fans in Melbourne and around the world. Back home, she was a huge hit.
"The Chinese fans were prepared to express their feelings and shed their tears of excitement. We were just one step from victory," China Central Television announcer Tong Kexin said Saturday. CCTV predicted that about 15 million people would watch the match live on its sports channel.
Li maintained her sense of humor even after the loss, saying she joked in the locker room that tennis matches should only last one set.
"I think I played great tennis, but she played better than me," Li said.
Clijsters led 4-2 in head-to-head meetings before the match, but Li beat Clijsters in the Sydney International final two weeks ago after the Belgian player had led 5-0 in the opening set.
Li and Clijsters joked and smiled with each other outside the dressing room before the match. Li seemed uncharacteristically nervous in her pre-match TV interview, and it seemed to translate to the court.
Clijsters opened the match with an ace, winning the first game on four straight points, then breaking Li the same way for a 2-0 lead. But Li found her range and appeared to steady her nerves in the third game, breaking Clijsters and holding for 2-2.
The turnaround continued when Li saved two big break points, then broke Clijsters in the final game of the set. She set up two set points with a stinging forehand that Clijsters didn't bother to run for, then two points later stunned Clijsters with a crosscourt forehand to close out the first set in 38 minutes.
There were four straight service breaks to open the second set before Li held to lead 3-2. Then Clijsters held for the first time in four games to tie the set at 3. Clijsters, with a backhand winner to the open court, broke Li in the next game to go up 4-3.
After that service break, Li went up to chair umpire Alison Lang of Britain and asked: "Can you tell the Chinese don't teach me how to play tennis?" That was in reference to some in the crowd yelling. They were saying "finish her" and "beat her" and later "calm down" in Chinese, which seemed to bother Li.
Li also snapped at her husband and coach, "Stop shouting at me."
Clijsters, who lost her serve in four straight games from the end of the first set, staged a remarkable turnaround, holding serve to open the deciding set and breaking Li's serve to take a 2-0 lead, just as she had in the opening set.
The Belgian player went up 3-1 when Li again lost her service for the seventh time in the match, then held in the next to go up 4-1.
Serving for the match at 5-3, Clijsters finished as she started it, taking four points in a row and winning the title when Li's last forehand landed wide.
After walking back to her chair, Clijsters buried her head in a towel. Li also had tears in her eyes on the other side of the court.
Clijsters explained those post-match tears.
"They're all emotional," Clijsters said. "I think what overwhelms me is that it's so intense up until that last shot, and then all of a sudden it's finished. Then it's just like a big relief. The disbelief maybe a little bit that it's over and that I was able to turn it around is what makes it all so special."
The Bryans have held the No. 1 ranking in doubles for the past eight years and have won 10 Grand Slam doubles titles, including the U.S Open three times and the French Open and Wimbledon once each.
The American brothers won the Australian title in 2006, '07, '09 and last year. They have been runners-up twice, but didn't lose their serve and broke the Indian team twice. They celebrated the win with their familiar chest bump.