An unusually large and unruly protest against the government of President Vladimir V. Putin ended here Saturday in clashes with the police and the arrest of opposition leaders. Rally organizers and the police said more than 100 people were arrested after a midafternoon scuffle between marchers and riot police on the main street, Nevsky Prospekt, in the heart of the city’s tourist district. St. Petersburg, Russia’s second-largest city, is Mr. Putin’s hometown. Two leaders of what is left of Russia’s liberal opposition, Garry Kasparov, the former chess grandmaster, and Mikhail A. Kasyanov, a former prime minister, spoke to the crowd. Then the protesters, accompanied by Mr. Kasparov, marched most of the length of the street, pushing through three police cordons as sirens wailed and Interior Ministry riot police scrambled to block their path.