Clijsters had to save four match points and defy an ankle injury to again get the better of Li Na in a repeat of last year's final.
Wozniacki had a much easier time of it, beating Jelena Jankovic 6-0 7-5 in a match which belatedly sparked into life.
And while the Dane was largely impressive, the performance of the day came from Clijsters, who won 4-6 7-6 (8/6) 6-4 in over two hours of absorbing tennis.
That the match went that far was testament to Clijsters' spirit as a nasty ankle sprain in the seventh game looked as though it could result in a retirement.
The 11th seed, in her final year on tour, carried on but her efforts looked to have been in vain when Li moved 6-2 up in the second set tie-break only to choke horribly when on the cusp of a last-eight slot.
Clijsters took full advantage of her opponent's meltdown to edge the third set, despite some anxious moments, and reach the quarters in Melbourne for a seventh time.
In a tournament of mis-matches, this always promised to be a classic but the weight of expectation seemed to affect both players early on with four breaks of serve in the opening five games.
Yet the drama was not long in coming as on the fourth point of the seventh game, Clijsters went down clutching her left ankle on the baseline.
The signs did not look good but after a medical time-out during which some heavy strapping was applied she was able to carry on and even win the game.
But with Clijsters' movement restricted Li seized her chance and a break at 4-4 handed her the chance to serve it out
Another break early in the second strengthened the Chinese's position and she appeared to have control of her emotions when she withstood some heavy Clijsters pressure to go 3-1 up.
But the defending champion was not done and came again to level the score at 3-3.
Despite frayed nerves it remained on serve until the tie-break which Li controlled to establish four match points.
Three came and went but on 6-5 it seemed all over when the fifth seed chased down a woeful Clijsters drop shot only to pat the ball tamely back into court, allowing her opponent to execute an inch-perfect lob.
Two points later and Clijsters had levelled the match as Li's game disintegrated.
The third set was a procession for the first four games as Li's focus went AWOL.
But, to her credit, she battled back, reclaiming one of the breaks as Clijsters failed to serve it out at 5-2.
But there was no reprieve second time round as the 28-year-old finally got the job done when Li netted a cross-court backhand.
Earlier, third seed Victoria Azarenka became the first woman through to the last eight courtesy of a straight-sets win over Iveta Benesova.
The Belarusian has yet to drop a set and was again impressive in beating Benesova 6-2 6-2 in 77 minutes.
She will next meet Agnieszka Radwanska, who strolled to a lop-sided 6-1 6-1 defeat of Julia Goerges.
The Pole's consistency proved key with just three unforced errors compared to 27 from Goerges, who sprayed the ball all over Hisense Arena.
Australian Open Day 7 Women's Fourth Round Results