Film actress Naznin Akter Happy made the rape allegation in December last year, having also said the 25-year-old Rubel had reneged on a promise of marriage that he made while they were having an "intimate affair".
Happy had told media in March that she was withdrawing the claims, one day after Rubel starred in a dramatic victory over England at the World Cup held in Australia and New Zealand. But she later pursued the case.
Rubel's lawyer Moniruzzaman Bhuiyan said the court ruling was based on the fact police found no evidence of semen on items in the cricketer's apartment following the complaint.
"The items were collected from Rubel's apartment after Happy lodged the complaint."
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"A forensic report also found no evidence of rape. So police had recommended that he be acquitted (of any charges)," he told AFP.
The allegation had threatened to scupper Rubel's chances of appearing in the World Cup after he was remanded in custody in January by a Dhaka court.
Happy's lawyer said he would lodge an appeal against the decision.
"It seems the judge was swayed by the stature of the cricketer and not by the merit of the case," Tuhin Hawlader told AFP.
Although victims of alleged rapes are usually entitled to anonymity, police waived reporting restrictions after Happy told the Bangladeshi media that she would drop the allegations if Rubel agreed to marry her.
Rubel has consistently rejected the allegation of rape or claims that he had offered to marry Happy, instead accusing her of "blackmail".