Mounted police stopped protesters from confronting the torch relay in the troubled Downtown Eastside neighbourhood with officials quickly diverting the route and the relay continued.
The final leg of the torch's 45,000-kilometre, 106-day cross-country journey ended at the First Nations pavilion and was carried by Malcolm Crawford, an honours student from Musqueam First Nation.
Thousands of Olympic fans streamed to the streets of Vancouver to get a final look at the torch.
Arnold Schwarzenegger received the torch in Vancouver's Stanley Park before handing it on to former Olympic champion Sebastian Coe, head of the London 2012 summer Games organising committee.
One fan held a sign that read "The Torchinator" - a reference to Schwarzenegger's role in "The Terminator" - as the one-time bodybuilder, movie star and governor of California ran his leg.
Among the other torchbearers were former national football player Carrie Serwetnyk and five-time Olympian and silver medallist Charmaine Crooks.
There were no arrests or confrontations among the protesters, who chanted against the Games taking place on "stolen native land" from the aboriginal peoples.
The torch went into hiding in the late afternoon awaiting its continuation at BC Place Stadium in the evening for the opening ceremony for the winter Games and the lighting of the cauldron.
The identity of the final torchbearer remains a closely guarded secret.