The 19th seed handed the reigning US Open champion a 6-0 6-1 thrashing which lasted just 52 minutes.
Clijsters' error-riddled performance was an extreme shock, given the dream run she has had since making her comeback last August after two years in retirement.
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Before the match against Petrova, she had a 20-3 win-loss record in her comeback, with only one straight sets loss.
As well as winning the US Open in her third tournament back, she had shown excellent form leading into the Australian Open, winning the Brisbane International, where she beat countrywoman Justine Henin in the final.
She also had comfortable straight sets wins in the first two rounds in Melbourne.
Unforced errors
But while former world No.3 Petrova played an excellent match, the bigger factor was Clijsters' constant mistakes on both her serve and ground strokes.
The opening set lasted just 18 minutes, Clijsters winning just five points, throwing in four double-faults and 17 unforced errors.
The second set started in similar fashion before Clijsters finally found some touch to get on the scoreboard in the 10th game of the match.
The Belgian managed to make Petrova work hard to win the final three games but never seriously threatened to turn the match into a contest.
Petrova's victory destroys the possibility of what could have been a blockbuster quarter-final match-up between Clijsters and fellow Belgian Justine Henin, who is making her grand slam comeback.
Henin downed Russian Alisa Kleybanova in three sets earlier in the day to move into the fourth round.
