The Indian child was allegedly raped by the three suspects on November 11, and later dropped off at her home.
The parents, however, alerted the police on January 9 this year.
The court said it could not rely on the confessions to the police as they were made in the absence of a translator, and were incompatible with the forensic report, Khaleej Times reported.
"The confessions in the interrogations by the Public Prosecution do not also stand since they are incompatible with the technical reports. The verdict also relied on findings of a medical panel, which was formed by the Ministry of Justice to determine whether the girl was molested or not," the court ruled.
The three men, including two supervisors and a driver ? aged 26, 37 and 44, were released from detention today after spending three months in prison.
"Gems Education notes that the Dubai Court has reached a conclusion that no rape or molestation of one of its students by the accused in the case has occurred, thereby conclusively refuting assertions which appeared in certain sections of the media that Gems Education or Dubai Modern High School has failed to protect its students," a spokesperson for Gems Education told the media.
"These men are family men, fathers with young children, loving husbands who we understand have endured not only immense emotional but also physical suffering... Their character and integrity have been subjected to attack by many sections of the community, the statement said.
As soon as the case was reported, prosecutors in Dubai started questioning the three men accused and referred them to public prosecution.
Dubai`s Attorney General said the male suspects - the bus driver, the supervisor and his assistant, sexually assaulted the girl, a student of Modern High School, while she was on her way back home.
Chief Prosecutor Sami Al Shamsi, Head of Bur Dubai Prosecution, was supervising the investigation which is being conducted by prosecutor Ahmad Al Attar.
Dubai Police officials have also said that the school and bus company must appoint women on buses to take care of children.
"We would caution against people conducting trials by media, and remember that all accused are innocent until proven guilty. It is important to let justice take its rightful course," the Gems statement cautioned.