A Division Bench comprising Justices K T Shankaran and M L Joseph Francis allowed the bail pleas filed by the accused last month.
The lone convict in the case, Dharmarajan, who was absconding and was arrested recently from Sagar in Karnataka, is now in jail, to serve the rest of his life sentence.
The court rejected the government counsel's argument that the accused should first surrender before the trial court before their plea could be taken up by High Court.
The Supreme Court had stayed the 2005 High Court judgement acquitting the accused three months ago.
The case relates to the rape of a 16-year-old girl of Suryanelli in Idukki District in 1996. The victim, a school girl, was allegedly abducted and taken to various places and sexually exploited by different persons.
The victim had also sought a fresh probe against Rajya Sabha Deputy Chairperson P J Kurien, alleging that he was among those abused her. Kurien has rejected the charge.