Abdullah Abdullah took 45% of the vote in the first round and his main opponent Ashraf Ghani polled 31.6%. Six other candidates were eliminated.
Last week, key rival Zalmai Rassoul threw his support behind Abdullah Abdullah, boosting his campaign.
This comes as international forces prepare to leave at the end of 2014, BBC reported.
Dr Abdullah and Mr Ghani, will now face each other in a second round on 14 June. The result was finally announced after a lengthy complaints process involving the recounting of thousands of ballot papers.
But this has not changed the standing of the two leading candidates.
Both Dr Abdullah and Mr Ghani are ex-government ministers, very well known inside and outside Afghanistan.