Raila Odinga and Uhuru Kenyatta will face off at the ballot on October 17, IEBC has said.
The decision was arrived at after the Supreme Court of Kenya nullified the presidential results that were held on August 8.
"There shall be no fresh nominations in the envisaged fresh election. The petitioner before the Supreme Court ... Raila Odinga and his running mate Kalonzo Musyoka and the third respondent Uhuru Kenyatta and William Ruto shall be the only candidates," IEBC chair Wafula Chebukati said in a statement on Monday.
More on this: Raila likely to face only Uhuru in repeat poll
IEBC says it is revising the operational and procedural requirements for the fresh polls and will share details in the coming days.
In the disputed election, Uhuru allegedly won by 1.4 million votes against Raila.
This is the third time that Raila is vying for the top seat.
He lost in 2007 and 2013 citing voter irregularities.
Education CS Fred Matiang'i had asked the electoral agency to conduct polls before the national examinations.
Thirdway Alliance presidential candidate Ekuru Aukot has criticised IEBC for the decision to hold the polls with only two candidates.
"The decision by IEBC to lock out other presidential candidates out of the fresh polls is invalid, illegal, null and void. We are going to court," he tweeted on Monday.
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