Zardari remitted the remaining prison term of Das "on humanitarian grounds", presidential spokesman Farhatullah Babar said.
The remission was granted on the advice of the Prime Minister to "honour an appeal of the Supreme Court of India to the government of Pakistan", he said.
A two-judge bench of the Indian Supreme Court had appealed to the Pakistan government earlier this month to remit the remaining period of Das` sentence and release him on humanitarian grounds.
The court made the appeal in response to a petition filed by Das` brother Anand Vir.
Babar noted that Indian media reports had mentioned that the Indian judges had resorted to the "unusual step" of appealing to Pakistan to consider granting remission to Das on humanitarian grounds.
He also pointed out that Justice Markandey Katju had, in his judgement, quoted a couplet by Faiz: "Qafas uddas hai yaaro sabaa se kuch to kaho, Kaheen to beher-e-khuda aaj zikr-e-yaar chale".
Das` family has said that he was arrested by Pakistani security forces when he mistakenly crossed the border in July 1984.
According to official records, Das was sentenced to life imprisonment in June 1987 and was set to be released by the end of this year.
However, acting on the advice of the Prime Minister, the President today remitted Das` remaining term, Babar said.
"The President signed the remission advice in the wee hours of Sunday, soon after the invitation of Prime Minister Manmohan Singh was accepted and it was decided that Prime Minister Yousuf Raza Gilani will proceed to Mohali to witness the semi-final cricket match between the teams of the two countries," Babar said.
The Home and Interior Secretaries of India and Pakistan will meet in New Delhi on Monday for the first in a series of meetings under the umbrella of the "full spectrum of dialogue" between the two countries.
Monday`s meeting will mark the formal resumption of the bilateral peace process that was stalled in the wake of the 2008 Mumbai attacks, which were blamed on the Pakistan-based Lashkar-e-Taiba.