Shopkeeper Oxana Sevastidi, 46, was convicted in March 2016 over an SMS sent eight years earlier about a train carrying hardware towards neighbouring Georgia, months before Russia fought a brief war with the country.
The lengthy sentence sparked an outcry from rights activists, and Putin at his annual news conference in December last year called her sentence "quite a harsh approach."
The official pardon published by the Kremlin said it is motivated by "principles of humanity" and enters into force in five days' time.
Sevastidi said she exchanged messages with a Georgian acquaintance about this.
"I just sent a text message," she told Meduza.
Sevastidi was detained by the FSB security service in January 2015 and convicted after a trial held behind closed doors in the southern city of Krasnodar.
Sevastidi's imprisonment only became public in 2016 after a team of rights lawyers took up her cause, believing she was wrongly convicted.
Russian rights group Memorial in February declared her a political prisoner, saying she was jailed for talking about what she saw on the street.
The Supreme Court is set to rule on her case on March 15, Smirnov told Interfax news agency. She is currently in Moscow's Lefortovo jail.
In a similar case, a woman in a small town outside Moscow was arrested in 2015 after calling the Ukrainian embassy to say soldiers had left a nearby base and could be heading to the separatist conflict in eastern Ukraine, where Russia denies military intervention.
The woman was held in jail for two months but was freed and had treason charges against her dropped after a public outcry.
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