Nadezhda Tolokonnikova, 24, and Maria Alyokhina, 25, are serving a two-year jail sentence for performing a crude "punk prayer" against Putin and his ties to the Russian Orthodox church in Moscow's main cathedral.
The two women had been due for release in March but are now expected to be freed sooner under the amnesty, in part because both are mothers of small children.
The amnesty will also enable 30 people arrested in a Greenpeace protest against Arctic oil drilling to avoid trial - removing two irritants in ties with the West before Russia hosts the Winter Olympics in February.
But Putin said the amnesty was not drafted with the Greenpeace activists or Pussy Riot in mind. It was passed, he said, to mark the 20th anniversary of Russia's post-Soviet constitution.
"It (the amnesty) is neither linked to Greenpeace, nor this group (Pussy Riot)," he told an annual news conference.
The Kremlin leader made clear he had no doubts about Russia's handling of both cases although it drew criticism from Western nations and a number of global celebrities.
"I was not sorry that they (the Pussy Riot members) ended up behind bars," Putin said. "I was sorry that they were engaged in such disgraceful behavior, which in my view was degrading to the dignity of women."
"They went beyond all boundaries," he said.
By freeing Pussy Riot members and Greenpeace activists, Russia is removing two of many irritants in ties with the West before Russia hosts the Winter Olympics in February. Concern over Russia's treatment of gays is already threatening to cloud the atmosphere at the Sochi Games.
The State Duma, or lower house, unanimously approved the amnesty proposed by President Vladimir Putin to mark the 20th anniversary of the passage of Russia's post-Soviet constitution. Human rights activists say the amnesty is far too narrow, freeing only a tiny fraction of Russia's more than half a million prisoners.
It will not benefit prominent Putin foes such as jailed tycoon Mikhail Khodorkovsky or opposition leader Alexei Navalny, who will be kept out of elections for years by a theft conviction he says was politically motivated.
The arrest of the men and women, dubbed the "Arctic 30", also drew Western criticism and was widely seen as a signal that Putin will not tolerate efforts to stop Russia's development of the resource-rich region where nations are vying for clout.
A lawyer for Tolokonnikova and Alyokhina, said she hoped the Pussy Riot band members would walk free within days.
"It's a very narrow amnesty. I'm very glad it applies to my clients," lawyer Irina Khrunova said by telephone.
The amnesty will take effect when it is published in the official government gazette, which is expected on Thursday.
The "Arctic 30" were arrested after Russian coast guards boarded the Greenpeace icebreaker Arctic Sunrise following a Sept. 18 protest in which some of the activists tried to scale Russia's first offshore oil platform in the Arctic.
They were charged with hooliganism, jailed in stark conditions for two months and have been unable to leave Russia since their release on bail.
"I might soon be going home to my family, but I should never have been charged and jailed in the first place," Greenpeace quoted Arctic Sunrise's U.S. captain Peter Willcox as saying.
"We sailed north to bear witness to a profound environmental threat but our ship was stormed by masked men wielding knives and guns ... We were never the criminals here."
A Greenpeace lawyer said it was unclear whether the foreigners, who do not have visas, could leave Russia by Jan. 1.
Putin, accused by his critics of curbing democracy during 14 years in power and stifling dissent in his third presidential term, said last month the amnesty should "underscore the humanism of our state".
It would release many elderly and young people, women with young children and people with disabilities.
But members of Putin's own human rights council estimate it will free fewer than 1,500 convicts. Almost all Russian trials end in convictions and the prison population is nearly 700,000.
Critics also say it could lead to the release of some police, soldiers and government bureaucrats charged with crimes, but will leave in jail people accused of violence against police, including protesters at a anti-Putin rally last year.
(Writing by Alissa de Carbonnel. Additional reporting by Maria Tsvetkova, Editing by Timothy Heritage and Alistair Lyon)