In August a year ago, the Court of Appeal sentenced them to six to eight months in prison, prompting the trio to challenge the decision in the CFA.
Wong, Nathan Law and Alex Chow were jailed in August previous year for their role in the mass pro-democracy Umbrella Movement protests of 2014 after Hong Kong's government pushed for more severe sentences.
Wong and Law were initially sentenced to community service, with a suspended sentence for Chow, over a September 2014 demonstration that saw protesters storm into Hong Kong's government complex.
On Friday, it was learned that the three activists, as well as the pro-democracy group behind the Umbrella Movement, have been nominated for the 2018 Nobel Peace Prize, a first for Hong Kong.
But this non-jail sentence was challenged by Hong Kong's Department of Justice that pushed for a review, eventually leading the Court of Appeal to impose jail terms.
In a summary of the judgment issued to the media, the five judges unanimously said it had "quashed the sentences of imprisonment" by the Court of Appeal.
Hong Kong, a former British colony, returned to Chinese rule in 1997 with a guarantee of wide-ranging freedoms, including freedom of speech, but critics accuse Beijing of creeping interference in the city's affairs and the government of toeing the Beijing line.
"It's not a time for celebration ... What we are up against is the court taking a very narrow definition of non-violent civil disobedience actions", said Wong.
"Maybe more and more activists will be locked up because of this harsh judgment", Wong, 21, told reporters on the courthouse steps after the decision.
Rights experts and legal analysts warned the case could have a "chilling" effect, creating a more lenient threshold for jailing dissidents and endangering political liberties. He said the fight for democracy would continue.
According to the report by Reuters, dozens of other democracy activists have been jailed or are facing court proceedings that could see them sent to prison for various forms of rights activism, "in what some see as a concerted attempt by authorities to curtail the momentum of the city's youth-led democracy movement".
Law called the result a victory for the three of them but a defeat for Hong Kong democracy as they would definitely face heavier sentences should the same initiative take place at present. The ruling "set a unsafe precedent for sending people to prison for protesting in the future", says Maya Wang, senior China researcher for Human Rights Watch.