On June 4 that year, the Chinese government sent troops and tanks to crush protests calling for political reform in and around Beijing's Tiananmen Square.
The death toll remains unknown, and discussion of what happened is censored in mainland China.
Rubio told a news conference on Wednesday that "no amount of censorship can erase the past".
"Those who sacrificed to uphold their unalienable rights of free expression and peaceful assembly will be vindicated someday," he said.
China's foreign ministry said Thursday it firmly opposed Rubio's comments.
"The Chinese government has long since reached a clear conclusion regarding that political turmoil that occurred in the late 1980s," ministry spokeswoman Mao Ning told a regular news briefing.
"The relevant erroneous remarks by the US side distort historical facts, smear China's political system and development path, and interfere in China's internal affairs," she said.
This year, authorities reportedly prevented the families of those who died in 1989 from visiting their graves at Beijing's Wan'an Cemetery, with Amnesty International calling the move "a heartless act".
- Hong Kong police presence -
Beijing has also moved in recent years to snuff out all public commemorations in Hong Kong, where an annual candlelight vigil had been held for decades before the imposition of a national security law in 2020.
As in previous recent years, AFP reporters saw a heavy police presence on both Wednesday and Thursday near Hong Kong's Victoria Park, the former site of the event.
Dozens of police officers were deployed, with roadblocks on the streets, and plainclothes officers stopped and searched some activists.
In the nearby Causeway Bay shopping district, a woman who made hand gestures representing the numbers six and four was taken away by police.
Chan Po-Ying, former leader of the disbanded pro-democracy group League of Social Democrats, was also led away to a police van.
She was swarmed by reporters as she walked around holding a yellow paper rose, which officers told her to put away.
"What we can do now is very, very little... Victoria Park holds 37 years of Hong Kongers' collective memory. I hope that we won't forget this collective memory," Chan told reporters before she was detained.
Alfred Tian, 29, said he made a special trip from the Chinese mainland to walk around the park and pray for the victims.
"As a Chinese, when you learn that history... I think at first it really strikes you because most Chinese people don't really know much about it," he said.
"It's like a fire in the heart, the pursuit for democracy, for freedom of speech."