The relay saw thousands of cheering flag-waving Chinese demonstrators vastly outnumber rival protesters, amid isolated scuffles between them.
About 300 anti-China activists were vastly outnumbered by more than 6,000 pro-China demonstrators, according to police estimates.
The protests were over China's forced repatriation of North Korean refugees and its security crackdown in Tibet.
Police deployed 8,300 anti-riot officers to guard the torch relay along the 24km route from Olympic Park to City Hall.
They warned that anyone trying to disrupt the relay would be reprimanded.
Despite the warning, sporadic clashes broke out between groups of several hundred flag-waving Chinese students and about 50 demonstrators critical of Beijing's policies.
The pro-Beijing protesters threw stones and water bottles at a Korean group that raised banners criticising Beijing. No injuries or arrests were reported.
The relay has also been viewed as an opportunity to address the issue of China's policy of deporting North Koreans caught fleeing their impoverished homeland.
"While trying to improve its image with the Olympics, China keeps sending defectors to the North knowing they would be executed or sent to political prisons," Ham Chang Kwon, head of a coalition of groups representing North Korean defectors in the South, said.
North Korea arrival
The torch has since arrived in North Korea for its first-ever run in the communist country.
Al Jazeera's Hamish MacDonald says the authorities are promising an "amazing" display in North Korea.
No disruptions are expected in the authoritarian state that does not tolerate dissent.
The torch's celebratory tour of 20 countries have turned into what analysts describe as a public-relations disaster for Beijing.