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World No. 2 and top seed Sabalenka came into the contest on a 15-match winning streak in Australia but was outplayed by former Wimbledon champion Rybakina.
Nadal said the pain is in the left hip, which caused him to miss so much time away from the court, but it may not be the same issue.
The 22-time Grand Slam champion overpowered Kubler in 83 minutes to book his place in the last eight.
Nadal marked his singles comeback after hip surgery with a victory over Austrian former world No. 3 Dominic Thiem in the Brisbane International first round..
However, Nadal showed no obvious after-effects of the hip injury that ruined his year.
The 22-time Grand Slam champion has not played a competitive match since bowing out in the second round of this year's Australian Open when hampered by a hip flexor problem.
Results 1-6
