After Hong Kong, the flame will complete the remainder of the relay through mainland China before returning to Beijing in time for the Olympic opening ceremony on August 8.
Al Jazeera's Tony Cheng, said: "This was the last chance for protesters to air their unhappiness before the torch gets to Beijing ... but we didn't seen any serious disruption.
"There were angry voices, there were raised voices, but we didn't see any violence."
During Friday's run, groups of Chinese university students waved national flags in front of pro-Tibet protesters, shouting and singing the national anthem to try to drown them out.
Human rights activists had vowed to take advantage of Hong Kong's special freedoms to criticise China's policies.
But the government, known for allowing public expressions of dissent, blocked several people from entering the former British colony, including three pro-Tibet campaigners and a Danish artist and rights activist.
The Hong Kong Journalists Association and other advocacy groups condemned the curbs and blamed behind-the-scenes pressure from Beijing for tainting the city's free and open image.
On Thursday Mia Farrow, the Hollywood actress and human rights campaigner, was questioned by immigration authorities before being allowed into Hong Kong, after being told disruptions to the torch relay would not be welcome.
Hong Kong has different laws from mainland
China on freedom of expression [Reuters]
Farrow, who has been pushing for China to do more to stop violence in the Darfur region of Sudan, said she planned to speak out against China's policies while in Hong Kong.
Al Jazeera's Cheng, who is in Hong Kong, said: "This is perhaps the first true test of the one country two systems ideology on which Hong Kong was founded.
"With Beijing watching so closely, it's hard for the city’s government to stand up for its rights."
Since Hong Kong's return to China from colonial rule in 1997, the main land rulers have promised the province a wide degree of autonomy under this political arrangement.
Debby Chan, a member of the Hong Kong-based Tiananmen Mothers campaign, said: "We also support the Olympics, but we just want to make the additional point that China must live up to its human rights promises."
Her group is pushing for the government to give a full and open account of the crackdown on pro-democracy protesters in Beijing's Tiananmen Square on June 4, 1989,
Authorities and business groups in Hong Kong have been striving to emphasise the city's pride, and enlisting tens of thousands of citizens to join Olympic celebrations.
Spectators for Friday's relay were encouraged to wear red to show their support for the torch, and about 3,000 police were deployed along the torch route.