The loss also stripped the Dane of her number one ranking in the process.
Showing no signs of the ankle injury sustained in her thrilling fourth-round win over Li Na - a match in which she had to save four match points - the Belgian had too much know-how for Wozniacki, whose search for a maiden grand slam title goes on.
It looked plain sailing for a rampant Clijsters as she raced into a set and 5-2 lead only for Wozniacki to launch an impressive fightback.
But it proved in vain, Clijsters' greater experience shining through as she clinched a 6-3 7-6 (7/4) win and a last-four spot against Victoria Azarenka.
"It definitely didn't feel like I was up a set and 5-2, Caroline is a very consistent player and a fighter and she became more aggressive," said Clijsters.
"I am happy to get through and not have to go to a three-setter as it's so hot."
The result will add weight to the argument of those who believe Wozniacki was not worthy of top spot, with the legendary Martina Navratilova on Monday demanding the WTA overhaul the current rankings system.
The 22-year-old has been at the summit for 67 of the past 68 weeks but the door now opens for Petra Kvitova, Azarenka and Maria Sharapova with the identity of the new number one determined by how the next few days in Melbourne pan out.
And while Clijsters, seeded 11, is some way adrift due to her injury-enforced absences, she showed enough today to prove she belongs among the elite.
She set the tone early on by breaking in the first game and, although Wozniacki hit back, further breaks in the third and seventh games handed her the opener on her fifth set point.
And when she broke twice more for a 5-2 lead it looked all over.
But Wozniacki fought back as Clijsters' hitherto flawless game started to crumble amid a flurry of unforced errors.
Having taken it to a breaker, however, Wozniacki ran out of steam and Clijsters regrouped to come through.