Officials said the man was on a lunch break from his job as a cleaner when he was hit in the head by "hard objects hurled by masked rioters".
It comes as China's president Xi Jinping said the "one country, two systems" system was being "challenged".
Hong Kong has been dogged by more than five months of political unrest.
Less than a week ago, Alex Chow, a 22-year-old student, died after falling from a building during a police operation.
What happened to the man?
The 70-year-old cleaner was hit in the head during a protest on Wednesday in the Hong Kong border town of Sheung Shui.
Video purported to be of the incident shows two groups throwing bricks at each other before the man falls to the ground after being struck on the head.
A police superintendent told news outlet SCMP that he was not involved in the protest, but was "only taking pictures at the scene".
He died in hospital on Thursday.
The Food and Environmental Hygiene Department (FEHD) said the man was an outsourced worker of theirs who had been on his lunch break.
The FEHD also condemned masked rioters, calling them "extremely dangerous".
"[They] conducted violent acts in various districts three days in a row, where they wantonly assaulted other members of the public," the statement added. "The acts are outrageous."
Hong Kong has seen an escalation in violence this week, with intense street battles, violent clashes at universities, and flashmob lunchtime protests.
On Monday, a police officer shot an activist in the torso with a live bullet, and a man was set on fire while arguing with anti-government protesters.
Image copyrightAFPImage captionHong Kong has been rocked by violence for months
What did President Xi say?
President Xi, who was speaking at a summit of BRICS countries in the Brazilian capital Brasilia, issued a strong warning to protesters.
He said that "radical violent activities" in the city had "seriously challenged the [principle of] 'one country, two systems'".
According to state media outlet the Global Times, Mr Xi said the "most pressing task for Hong Kong is to end violence and chaos and restore order".
He also threw his "firm support" towards the Hong Kong police force.
Why are there protests in Hong Kong?
Hong Kong - a British colony until 1997 - is part of China under a model known as "one country, two systems".
Under this model, Hong Kong has a high degree of autonomy and people have freedoms unseen in mainland China.
The protests started in June after the government planned to pass a bill that would allow suspects to be extradited to mainland China.
Many feared this bill would undermine the city's freedoms and judicial independence.
The bill was eventually withdrawn but the protests continued, having evolved into a broader revolt against the police, and the way Hong Kong is administered by Beijing.
Protests have taken place every weekend over the past few months, causing widespread disruption.