As Beijing celebrated 70 years of communist rule, the semi-autonomous territory to the south was swamped by anti-government demonstrations.
An 18-year-old was shot by police at close range in one incident, with police saying the officer had fired because he feared for his life.
Police spokeswoman Yolanda Yu said the protester was hit on the left side of his chest with a single pistol shot.
Video posted on social media appeared to show an officer firing at a protester who had come at him with a metal rod.
There were no details given about the second critical case.
Hong Kong’s hospital authority confirmed it was treating two people in critical condition and that 51 others had been injured in the clashes.
Sky’s Siobhan Robbins, who is in Hong Kong, said the shooting was “a turning point”, adding: “Although we’ve seen officers firing live warning shots in the last few weeks we haven’t seen a protester directly hit.”
Joshua Wong, one of those leading the protesters, said on Twitter that Hong Kong had “fallen into a de facto police state”.
He added: “To a murderer (who) celebrates in bullets and bloodshed, lip service alone is no longer coercive. The world must step up concrete actions against this brutal regime.”
Organisers said around 100,000 people had joined the protests, despite a police ban, but there was no crowd estimate supplied by police.
Many subway stations and shopping centres were closed due to the violence, as police used tear gas in at least six locations and water cannons in the business district and protesters threw petrol bombs and bricks in retaliation.
King Chan, a 57-year-old who came to protest with her husband, said of the police: “They are squeezing our necks so we don’t breathe the air of freedom.”
Fellow protester Bob Wong, 40, said his black clothing expressed “mourning” for “the death of Hong Kong’s future.”
The protests began in June as a reaction to a now-abandoned bill that would have seen those suspected of crimes in Hong Kong facing extradition to China.
But over the past few months, the campaign has widened to encompass general anti-China feeling in the city, as residents fear their freedoms are being eroded.
Hong Kong retained those freedoms, which are not enjoyed by those on the Chinese mainland, after the former British colony was returned to China in 1997.