The global campaign, launched to coincide with the Athens Olympics, hit screens at the weekend and shows the girls turning into Serena Williams to impress their coach.
However, pressure groups called for the ad to be pulled after high-profile coach Gavin Hopper was jailed for three-and-a-half years for indecently assaulting a 14-year-old student in the mid-eighties.
Hopper, jailed 10 days ago, coached top players such as Monica Seles and Mark Philippoussis.
Joe Tucci, the chief executive of the Australian Childhood Foundation, said the ad "trivialised" the experiences of young women who had been abused.
"Advertising needs to reflect a better sensitivity to respectful relationships between adults and kids and I don't think this ad does," he told Australian Broadcasting radio.
Nike apologised for any offence caused by the commercial but said it planned to run the ad elsewhere in the world, including the UK.
Tony Balfour, the managing director of Nike Australia, said: "We have decided to axe the commercial given current community concerns regarding recent events and our own position on the matter."
Last month Nike US was deliberating whether to run an ad featuring five-time medal-winner Marion Jones, the track and field athlete investigated by the US anti-doping agency.
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