Kenyan lawmakers passed the vote in a special session of parliament boycotted by opposition members who stood outside shouting at passing members of the ruling Jubilee coalition.
The vote took place as Raila Odinga, former prime minister and leader of the CORD opposition alliance, was trying to block it in a Nairobi court.
"India, which is one of the largest democracies in the world, registered 863 million people biometrically, and also used EVID (Electronic Voter Identification System) in the elections and it worked without any problem, why can't Kenya do the same?" said Odinga.
Odinga warned that "if there is no democratic election then there will be no elections in Kenya".
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He called for protests to start on January 4.
"Let Raila Odinga know that his threats won't work because we have no law in Kenya saying that there can be no elections unless Raila is on the ballot," said leader of the majority in parliament Aden Duale.
The parliamentary session was held under tight security in the presence of anti-riot police, and at a point in the debate, the live broadcast was switched off. Journalists reported far more limited access than usual.
CORD unleashed a protest campaign which turned violent in May and June in a bid to force change among the members of the IEBC -- whose nine commissioners finally stood down in October.
The 2017 election is shaping up as a replay of 2013, with 71-year-old Odinga aiming to unseat Kenyatta, 55.
It will be the third attempt by Odinga -- son of the first vice president of Kenya -- to win the presidency.
Violence after that election quickly split along tribal lines and left more than 1,100 dead.