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Gunathilaka was found not guilty of sexually assaulting a woman in Sydney when he was in Australia last year for the Twenty20 World Cup.
Gunathilaka had to surrender his passport during the trial but is free now to return to Sri Lanka, media reported.
Gunathilaka entered a not guilty plea to the remaining charge of sexual intercourse without consent at a local court in Sydney on Thursday.
Sri Lanka Cricket, the national governing body, had launched an inquiry into alleged misconduct by the 27-year-old and had suspended him from all forms of international cricket at the conclusion of the second Test against South Africa.