Wong, Nathan Law and Alex Chow were sentenced to six months, eight months and seven months respectively after the Court of Appeal upped their previous non-custodial sentences.
Activists say the case is more proof that Beijing is tightening its grip on the semi-autonomous city.
Wong shouted: "Hong Kong people, don't give up!" as he was led away by security.
Hong Kong enjoys much greater freedoms than on the mainland, with its liberties enshrined in the handover agreement made when the city was given back to China by Britain in 1997.
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All three defendants were found guilty last year on unlawful assembly charges for storming a fenced-off government forecourt known as "Civic Square" as part of a protest calling for fully free leadership elections in September 2014.
Their arrests sparked wider rallies which exploded two days later when police fired tear gas on the crowds, triggering mass demonstrations that brought parts of Hong Kong to a standstill for more than two months in an unprecedented challenge to Beijing.
Wong and Law received community sentences and Chow a three-week suspended sentence at magistrates' court last August over the Civic Square protest.
In emotional scenes before the judgement, tearful supporters hugged the three and chanted: "Shame on political persecution!"
Around 20 pro-Beijing supporters shouted back through loudspeakers, chanting "Pay the price in jail!"
Ahead of the judgement today, the department of justice said there was "absolutely no basis to imply any political motive" on its part in relation to the case.