The decision to approve the nomination of Edward Yiu today, hours before the deadline, came two days after fellow pro-democracy candidate Agnes Chow, 21, was barred from standing because her party supports self-determination for Hong Kong.
Around 2,000 people gathered outside government headquarters last night to protest at Chow's disqualification.
Yiu said his approval was "absolutely not worth rejoicing over" in light of the government's "evil acts".
"I'm really very, very angry because it reflects that the government has manipulated the whole system, trying to control the result of the by-election," Yiu told reporters.
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China sees self-ruling Taiwan as part of its territory and has threatened military attack if it ever declares formal independence.
Beijing is also increasingly incensed at what it sees as threats to its sovereignty over semi-autonomous Hong Kong.
It has rights unseen on the mainland including freedom of speech and a partially elected legislature, but there are concerns liberties are being eroded. Since the mass Umbrella Movement rallies of 2014 failed to win political reform, some activists are demanding independence for Hong Kong.
Chow's party Demosisto also does not advocate independence outright but campaigns for self-determination, pushing for a referendum to allow citizens to choose how they are governed.
Yiu became a lawmaker in 2016 but was among six opposition legislators disqualified for inserting protests into their oaths of office.
Hong Kong's leading lawyers weighed in on the saga today, calling the move to ban Chow "unreasonable, unlawful and unconstitutional" in a joint statement signed by 30 attorneys.
"Disqualification of candidates with certain political opinion or affiliation frustrates the core purpose of an open and fair election, which is to guarantee the free expression of the will of the electors," it said.