Raila Odinga, a veteran politician and leader of the National Super Alliance (Nasa), had been expected to boycott the poll.
The High Court ruled on Wednesday that returning officers had been improperly appointed.
It is the latest in a series of irregularities surrounding the election, which is a re-run of a poll in August that had already been annulled by the Supreme Court.
The last election saw the incumbent Uhuru Kenyatta re-elected by a small but comfortable majority.
The new round has been marred by opposition claims of continued flaws, the flight into exile of an election commissioner and an admission from the head of the electoral board that they were not ready.
And on Tuesday night, the day before the Supreme Court was due to hear a petition to postpone voting, the bodyguard of the deputy chief justice was shot and wounded.
The election will go ahead as there were not enough judges on the bench to hear the case the next morning.
Amid this mayhem, the Commonwealth has withdrawn its observers, the European Union has scaled its election operations back and the international community has repeated its calls for "calm".
@TheGlobe reporters.
But Mr Odinga clearly attempted to seize an historic moment.
He told his supporters in Nairobi's Uhuru Park that Kenya had an obligation to all Africans to stand in the way of the trend towards elected autocracy on the continent.
And then he went on to make this declaration: "One, from today we will transform a national coalition into a resistance movement.
"Two, we will embark on a national campaign of defence of the legitimate government with authority and then put pressure to all its organs.
"Three, boycott the goods and services offered of the businesses who benefited (inaudible) being established.
"Four, we shall convene a people's assembly for the purpose of judging our way back to constitutional rule and democracy.
"Five, we shall mobilise all progressive forces in the country to ensure that a fresh, free and fair presidential election is organised within 90 days."
This sets him and his supporters who make up a substantial part, if not a majority, of Kenya's political body on a collision course with the government.
Calling for both resistance and the establishment of a parallel government of some kind takes the country into dangerously populist territory, even if he has the legal basis for his claims of election chaos.
More than 1,000 Kenyans were killed in political violence after the 2007 polls.
The bloodletting was blamed largely on Mr Kenyatta and Henry Ruto - who were then rivals but now share power.
Mr Odinga's calls were met with wild enthusiasm by his hard core of supporters - many of whom attended the rally lured in by the prospect of free t-shirts and hats.
They then went on to march through town back to the poorer parts of Nairobi where his support base is strongest but also where tribal rivalries divide communities.
Tyres were set alight and there were reports of some attacks on motorists.
But heavy rain damped the political fires.
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