Any doubts over the Belgian's injured ankle were erased with a sparkling centre court performance.
It was only the fourth time the world number two had whitewashed an opponent in a Grand Slam tournament.
"That was perfect," the second seed smiled on court. "It doesn't happen that often that you play so well. Really perfect.
"My ankle felt pretty good. It flared up a little yesterday but today it felt good."
Clijsters was joined in the winners' circle by third seed Venus Williams, who beat Russian Vera Douchevina 6-4, 6-2.
The American is playing her first tournament since she was struck down by an abdominal injury after losing last July's Wimbledon final to younger sister Serena.
In the men's field, Clijsters' fiancé Lleyton Hewitt overcame a slow start to comfortably beat Slovakia's Karol Kucera 1-6, 6-1, 6-4, 6-1.
Third seed Juan Carlos Ferrero survived two injury scares to battle past Italian Filippo Volandri 6-4, 7-6, 7-5.
The Spaniard received pain-killers and a rub-down from a trainer after twisting his back and he called for the trainer a second time after hurting his left elbow lunging for a volley.
Clijsters in contrast was unhindered by injury and in ominous form.
Runner-up at the French and U.S. Opens last year, she is seeking her first grand slam title and meets Dinara Safina in the next round.
"She is tough...hits the ball hard and plays well," Clijsters said. "I will have to be careful."
Teenager Safina led a raft of Russian women into the third round earlier on Thursday.
The younger sister of former world number one Marat Safin, Safina upset South Africa's Amanda Coetzer 7-5, 6-3 to post her best Melbourne Park result.
BIGGEST WIN
The 17-year-old was beaten in the first round last year but proved too good for 27th seed Coetzer.
Elena Likhovtseva emulated Safina by eliminating another seed in Francesca Schiavone, thumping the 18th-seeded Italian 6-2, 6-2.
Anastasia Myskina continued to cut through the draw with a straightforward 6-2, 6-4 win over Emmanuelle Gagliardi and Lina Krasnoroutskaya and Maria Sharapova completed the Russian quintet.
Saori Obata scored the biggest win of her largely uneventful career when she upset eighth seed Ai Sugiyama 6-4, 6-4 in an all-Japanese battle.
The 25-year-old from Tokyo scored her first win in four matches over her more famous compatriot to reach the third round here for the first time.
Briton Tim Henman beat Radek Stepanek 6-2, 4-6, 6-3, 6-0 to keep alive his dream of an elusive Grand Slam title.
A consistent performer, the 11th seed made the fourth round of the Australian Open from 2000 to 2002 but has never been able to go further.
"I felt like my game plan and my tactics were good and I was coming forward, you know, pretty much as much as possible," said Henman, who won 50 out of 73 points at the net. "I was very strong between the ears."
Wimbledon champion Roger Federer safely negotiated U.S. qualifier Jeff Morrison 6-2, 6-3, 6-4.
Melbourne favourite Mark Philippoussis opens the night session when he takes on tricky Frenchman Fabrice Santoro.
