In a statement, the agency said the bail was granted to Yousuf Chopan, who had been arrested by the NIA in a terror conspiracy case, and not the February 2019 attack case.
Both the terrorists, equipped with suicide vests and sophisticated weapons, were killed in the encounter on Friday, averting a major suicide attack in the city.
The NIA on Tuesday took over the case of last week's terror strike near an army camp Jammu, officials said, as one of the three arrestees confessed to transporting terrorists from the International Border to Kashmir in the past also, sending alarm bells ringing in the security establishment.