The court said Tolokonnikova's refusal to admit her guilt was the reason she would not be paroled, RIA Novosti reported.
Tolokonnikova, along with Yekaternia Samutsevich and Maria Alyokhina were arrested Feb. 21, 2012, after several Pussy Riot members gave a controversial performance at Moscow's Christ the Savior Cathedral.
"I will appeal my sentence to the last, up to the Supreme Court of the Russian Federation. I do not admit any guilt and will not do so. I do not consider that to be a bad thing, as the [prison] colony does, but a good thing, for I have principles upon which I will stand," Tolokonnikova said at the hearing.
Alyokhina's parole was also rejected, on Wednesday, the BBC reported.
Samutsevich was released in October after her lawyer argued she was seized by guards before she reached the altar during the protest at the church.