The commission said Friday that Mahamadou Issoufou, a prominent opponent of the ousted former president, took 36 percent of votes in Monday's poll. His party dominated local and regional elections last month.
He was trailed by Seini Oumarou, who served as prime minister under the overthrown president. Oumarou took 23 percent and will face Issoufou in a runoff. The commission says nearly 53 percent of voters participated in the impoverished West African nation.
President Mamadou Tandja was ousted in a coup last year by a military junta, after Tandja changed the constitution to stay beyond his term.