The narrow win for Issoufou, who is known as the "Zaki" or "Lion" in Hausa, the majority language in Niger, came yesterday after he had vowed to secure an outright victory in the first round.
His rivals had in turn pledged to unite behind whoever scored highest among them to challenge the 63-year-old's bid for a second five-year term.
The CENI election commission said Issoufou won 48.4 percent of the February 21 vote, with his nearest challenger Amadou picking up 17.4 percent.
Two other prominent politicians, former premier Seini Oumarou and ex-president Mahamane Ousmane, won 12.11 percent and 6.25 percent respectively.
Turnout was at 66.8 percent, CENI said.
Issoufou, who campaigned on pledges to boost the economy and keep the country safe from jihadist attacks, had hoped for a quick win but was a tantalising 167,000 votes short of the "knock-out" victory he had vowed.
The final round is due to be held before the end of March.
The opposition has accused the leader of corruption and of sowing discord among political parties to impose a dictatorship.
The former prime minister and national assembly president fled the county in August 2014 to escape charges in the matter but was arrested after he returned last November.
About 7.5 million people were eligible to vote in the elections, whose credibility was questioned by the opposition.
A total of 15 candidates ran for president in the impoverished country straddling the Sahara Desert, rocked over the past year by attacks by Boko Haram jihadists operating out of neighbouring Nigeria, as well as Islamist fighters in the north.
The African Union, which deployed 40 observers, has said it was generally satisfied with the organisation of the vote, despite the logistical glitches.
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