Lawyers say the amnesty will also enable 30 people arrested in a Greenpeace protest against Arctic oil drilling to avoid trial - removing an irritant in ties with the West before Russia hosts the Winter Olympics in February.
Putin has said the amnesty, passed to mark the 20th anniversary of Russia's post-Soviet constitution, was not drafted with the Greenpeace activists or Pussy Riot in mind.
Tolokonnikova's father Andrei told Reuters on Thursday that the planned release of the band members was clearly a public-relations move ahead of the Olympics.
"It is an absolutely cynical game of the central authorities," he said while awaiting her release from jail in the Siberian region of Krasnoyarsk.