Clijsters, only five tournaments into her own comeback that has already netted the U.S. Open title, saved two match points and wasted three before winning 6-3, 4-6, 7-6 (6) over the seven-time Grand Slam titlist.
Henin immediately withdrew from next week's Sydney International, saying she had strained her upper left leg and didn't want to risk further injury ahead of her Grand Slam return at the Australian Open, which starts Jan. 18.
Clijsters led by a set and 4-1 before Henin, who struggled early and had two double-faults to open her first service game, staged a dramatic rally.
Henin, playing in the top tier for the first time since she quit while holding the No. 1 ranking in May 2008, won the next eight games to take a 3-0 lead in the third.
Clijsters rallied to 3-3, then gave up a break and gave Henin match points in the 10th game.
Clijsters held her nerve and, 15 minutes later, held her arms in the air, celebrating what she thought was a championship-winning backhand down the line in the tiebreaker when the umpire overruled.
Henin got back to 6-6 in the tiebreaker but double-faulted to give Clijsters a fourth match point. She made no mistake this time, with a forehand that Henin couldn't get.
"Huh, what a match!" Clijsters told the crowd at Pat Rafter Arena. "I think we set the bar pretty high for ourselves for the rest of the year.
"It's a great tournament to start the year with. I couldn't be happier with myself."
The top-seeded Clijsters closed Henin's career lead to 12-11, ending the three-match winning streak that Henin had in 2006 -- maintaining a sequence in which no player won more than three straight.
Clijsters took more than two years off the tour and got married to American Brian Lynch and had a daughter, Jada, in February 2008.
She was only three tournaments into a comeback when she won the U.S. Open in September and became the first mother to win a major since Evonne Goolagong Cawley at Wimbledon in 1980.
Clijster's daughter and husband were in the crowd on Saturday, when she donated her tournament winnings to Brisbane's Royal Children's Hospital, which she had visited this week.
"I forgot how to make a speech!" she said, laughing. "It's just great to be back. I want to congratulate Kim. It was a great fight. I really enjoyed my time out here tonight. It couldn't expect more. It was a dream."
Henin said Clijsters had more recent experience in playing the big points, which was the difference Saturday.
"I'm so proud of what we did on the court today," she said. "I didn't play a tournament in 18 months and I've been able to compete with really one of the best players in the world. I can be happy.
"It was a drama from the beginning to the end."
Henin said it was the most intense match of their rivalry, which dates back to juniors.
"I have nothing to regret. We were both on the court wanting to win. It was just a good fight," she said. "I have to be positive of course. It's disappointing to lose. I would have preferred to win ... But at the end I remember that it's my first tournament back and I'm able to compete at a very high level."
Henin had wild card entries to Australian Open lead up events in Brisbane and Sydney, where she had a potential second-round meeting with top-ranked Serena Williams. Instead, she'll stay in Brisbane to recover and is confident of being fit for her first major since the 2008 Australian Open.
Roddick rallied for a 1-6, 6-3, 6-4 win over fourth-seeded Tomas Berdych of the Czech Republic in the semifinal Saturday.
Stepanek easily beat Frenchman Gael Monfils 6-2, 6-1 in an hour in the first semifinal.
Roddick dropped serve twice in the opening set against Berdych, when he didn't convert any of his four breakpoint chances. It was the first time in the tournament that his serve had been broken, ending a run of 30 straight winning service games.
But he rebounded in the second set, building a 3-0 lead with an early break. The third set was on serve until Roddick broke for a 5-4 advantage.
"I like to confuse and conquer sometimes," Roddick joked of his first-set lapse. "I didn't feel like I was hitting the ball that badly, but he played really well.
"The biggest part of the match was the first couple of games of the second set, where I didn't want to let him keep rolling ... to stop the momentum early in the second."