Organised by a group of veteran democracy activists, the vigil demands justice for the victims of the crackdown.
Semi-autonomous Hong Kong is the only place on Chinese soil to see a major commemoration of the military's brutal crushing of pro-democracy protests in central Beijing in 1989.
However, in the past two years, student unions have boycotted the longstanding vigil in Victoria Park as they say its message is increasingly irrelevant.
Organised by a group of veteran democracy activists, the vigil demands justice for the victims of the crackdown and also pushes for the democratisation of China.
Some young activists in Hong Kong say they want to prioritise the democratic future of the city itself and not China as a whole, as anti-Beijing sentiment grows.
Younger generations tend to see themselves as distant from mainland China, with some calling for more autonomy or even independence for Hong Kong after mass rallies for political reform in 2014 failed to win concessions.
Mak Kwan-wai, vice president of Hong Kong Baptist University's student union, told AFP that building a democratic system in China was not Hong Kongers' responsibility.
"What Hong Kongers should do is protect themselves," Mak added.
Baptist was among several universities whose student unions did not attend the vigil.
But democracy campaigner Joshua Wong, who led the 2014 pro-democracy rallies, said people should not forget the victims of June 4.
"I believe we all share the same goal, which is to demand that the central government take responsibility for the massacre," said 20-year-old Wong at the park.
He added it was particularly important to support the event as the city approaches the 20th anniversary of its handover from Britain to China on July 1, 1997.
China's President Xi Jinping is expected to visit as part of the celebrations.
In a statement marking the Tiananmen crackdown, US Secretary of State Rex Tillerson called on China "to respect the universal rights" of its citizens.
"We call again on China to make a full accounting of those killed, detained or missing due to the events of June 4, 1989," he said.
Mainland human rights activist, Wang Yan, 52, who has been living in Hong Kong for the past seven years, warned against complacency over Tiananmen.
"We have to keep persisting. If we give up, are we just going to let it go if people get killed in the future?" she told AFP at the vigil.
Organisers said 110,000 attended, down from 125,000 last year. Police put the crowd at 18,000. Turnout numbers given by activists and authorities always vary widely.
The park's six football pitches were filled with sombre crowds holding candles and phone torches aloft as they chanted and sang.
A big screen played footage of the Tiananmen crackdown and interviews with some of the mothers of the victims, while activists delivered tributes to those who died.
Hundreds of protesters, including Wong and other leading democracy activists, later marched from the park to China's liaison office, chanting "People will not forget", and demanding the release of political prisoners on the mainland.
They held 28 candles for a moment of silence outside the heavily policed building, before throwing them over the fence. Protesters also burned a Chinese Communist Party flag before dispersing.
On Chinese microblogging website Weibo, foreign account holders found themselves unable to publish any photos or video.
The Twitter-like site said the block, lasting from June 3 to June 5, was to "upgrade the system".
A small gathering of pro-Beijing supporters rallied near Victoria Park earlier in the day.
Their banners accused protesters at the June 4 commemoration and in 2014 of "using students as chess pieces" and denounced both as "despicable".
Scuffles broke out briefly among rival protesters before police separated them.
In downtown Taipei around 50 protesters gathered in commemoration and called for the release of activists on the mainland, including Taiwanese NGO worker Lee Ming-cheh who has been detained in China on subversion charges.
Taiwan's president Tsai Ing-wen urged China to release Lee in a message on her Facebook page.
She also asked Beijing to acknowledge June 4 and work towards democracy.