Police contingents repelled with tear gas and shots in the air around 1,000 demonstrators in the central area of this capital. In Kisumu city, local television showed running battles with stone-throwing youth.
Three other protesters had gunshot wounds in the confrontation in the Odinga stronghold of Siaya County, Bondo police chief Paul Kiarie said.
The government has mobilized security forces in Kisumu, Mombasa and Nairobi to keep in check opposition supporters despite the ban on such demonstrations.
In Nairobi, opposition legislators were repeatedly tear gassed as they tried to drive into the city centre.
He supported protesters' right to demonstrate, he said, but has so far stopped short of calling people onto the streets himself.
"This ban, announced just two weeks ahead of a fraught repeat presidential election, is likely to become a basis for heavy-handed police crackdowns", said Michelle Kagari, a deputy regional director with Amnesty International. The results of of those elections were overturned by the Supreme Court, after a lawsuit by the main opponent to President Uhuru Kenyatta, based on fraudulent manipulation when posting the vote-count results on the Web. "All indications are that the election scheduled for 26 October will be worse than the previous one", he said, announcing his withdrawal Tuesday.
The protests also kicked off the coastal city of Mombasa where opposition supporters peacefully marched in the streets before being dispersed by the police.
But Mr Odinga's withdrawal has left behind widespread confusion in East Africa's largest economy, with observers wondering how the new election might go forward.
"We will continue with our demonstrations as planned across the country", said one of the coalition's leaders Moses Wetangula.
Kenya's opposition leader Raila Odinga said on Friday that his withdrawal from a presidential election rerun scheduled for October 26 meant the poll had been "canceled" and there should be fresh nominations for a new vote.
The election commission has said the new vote will go ahead with all eight candidates who ran in August and that Odinga is still considered a candidate as he has not formally withdrawn.
The decision was a rare victory for Odinga, a veteran opposition leader who failed to win election in 1997, 2007 and 2013, claiming to have been cheated of victory in the latter two votes.
In a statement issued by Minister for Africa Rory Stewart on Friday, the United Kingdom government pointed out that the rushed amendments would bring unnecessary tension in the country. That judgement stated that if a candidate dies or withdraws from the fresh election, the IEBC must begin presidential nominations from scratch.