A bench headed by Justice Ranjana Prakash Desai refused to give any relief to Nithyananda.
The bench while hearing the case had on August 20 questioned the controversial godman for his reluctance to undergo the test, saying such examinations are becoming necessary day-by-day in view of rise in rape cases.
The bench had also said that there is no reason why an accused in a rape case should not be subjected to potency test and had questioned the police for delay in conducting the test in the 2010 case.
The apex court had on August 21 reserved its verdict on Nithyananda's plea.
Karnataka High Court had on August 1 stayed the non-bailable arrest warrant issued by a Ramanagaram court against Nithyananda and four of his followers in connection with the case.
The high court had directed Nithyananda to present himself before the investigating officer for the medical test and also to appear before the Chief Judicial Magistrate (CJM), Ramanagaram, on August 18.
It had passed the order on the petitions filed by Nithyananda and his followers questioning the July 28 order of the CJM.
They had claimed that the CJM was not justified in issuing the non-bailable arrest warrant against them as the high court in its July 16 order did not direct them to be present before the CJM on July 28 but it was the date given for the trial court to commence hearing in the rape case, which was pending from four years.
In its July 16 order, the high court had upheld the 2012 order of the CJM, who had allowed the plea of the Criminal Investigation Department to subject Nithyananda to medical test to find out whether or not he was capable of having sexual intercourse, and also to collect his blood and voice samples.
Observing that Nithyananda had been granted regular bail, the high court in the July 16 order had made it clear that he should be taken into custody only for the limited purpose of subjecting him to medical test and for collecting voice and blood samples, if he voluntarily failed to appear before the investigating officer.