Beijing said the vote went against Hong Kong's constitution and accused its organisers -- local democracy activists -- of breaching the rule of law.
Organised by the activist group Occupy Central, the informal referendum saw more than 790,000 people vote over 10 days on how Hong Kong's next leader should be chosen.
Beijing said the activists were determined to "pursue self-interests through breaching the rule of law, disturbing Hong Kong's social order and holding back the progress of universal suffrage".
Beijing has promised to let Hong Kong residents elect their next leader in 2017, but has ruled out giving voters a say in selecting candidates.
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This has fuelled fears among democracy advocates in the city -- a British colony until 1997 -- that only those sympathetic to Beijing will be allowed to stand. Hong Kong's current chief executive was selected by a 1,200-strong pro-Beijing committee.
Students are also planning a peaceful overnight rally in the Central business district as well as outside government headquarters.
"It's time to escalate our action and put pressure on the Hong Kong government and the central government," said student leader Joshua Wong.
Concerns have been growing that the freedoms Hong Kong was guaranteed under the "One Country, Two Systems" deal at the time of the handover are being eroded.