Known as a strong ally of Beijing, John Lee's appointment is being widely seen as a move by China to tighten its grip on the city.
A former security chief who oversaw the crackdown on Hong Kong's democracy movement was anointed the business hub's new leader by a small committee of Beijing loyalists.
John Lee, 64, was the only candidate in a Beijing-backed one-horse race to succeed outgoing leader Carrie Lam.
His elevation places a security official in the top job for the first time after a tumultuous few years for a city battered by political unrest and debilitating pandemic controls.
Despite the city's mini-constitution promising universal suffrage, Hong Kong has never been a democracy, the source of years of public frustration and protests since the 1997 handover to China.
Its leader is instead chosen by an "election committee" currently comprised of 1,461 people -- roughly 0.02 percent of the city's population.
After a brief secret ballot on Sunday, 1,416 members voted for Lee while eight voted against according to officials. The rest did not cast ballots.
"I declare that the only candidate Mr John Lee Ka-chiu is returned in the above mentioned election, congratulations," returning officer Justice Keith Yeung Kar-hung, announced.
Police forces on alarm
Protests have been largely outlawed in Hong Kong, with authorities using an anti-coronavirus ban on public gatherings of more than four people as well as a new national security law.
Police ringed the exhibition centre with security, and 6,000 to 7,000 officers had been placed on standby, according to local media.
The League of Social Democrats -- one of the only remaining pro-democracy groups -- held a three-person protest before polls opened, chanting "Power to the people, universal suffrage now".
"This is what John Lee's new chapter looks like, a shrinking of our civil liberties," said protester Vanessa Chan as dozens of police officers looked on.
"We know this action will have no effect, but we don't want Hong Kong to be completely silent," she added.
Under President Xi Jinping, China is remoulding Hong Kong in its own authoritarian image after huge and sometimes violent democracy protests three years ago.
Beijing deployed a sweeping security law to stamp out dissent and rolled out a new "patriots only" political system for Hong Kong to guarantee anyone standing for office is considered suitably loyal.