He secured the victory by a landslide in a contest opposition parties say was flawed by fraud and violence.
His party also won all 10 gubernatorial elections and more than 70% of seats in the national assembly.
His opponent, Ossufo Momade, the candidate for the main opposition party and former guerrilla movement Renamo attained 21.8% of the vote, said the Commission’s Chairman, Abdul Carimo at a news conference on Sunday.
The outcome puts Nyusi and his Frelimo party responsible of an economy that is preparing to receive more than $50 billion in investments in natural gas export projects with companies like Total SA and ExxonMobil Corp.
There is also a potentially fragile peace deal President Nyusi signed with Momade in August to permanently end fighting with the Mozambican National Resistance while battling Islamist insurgency in the country.
The Oct 15. presidential, legislative and provincial poll was hoped to set the seal on the deal which was designed to put a complete end to four decades of violence between Frelimo and Renamo.
However the deal is at risk of falling apart as opposition parties reject the results.
President Nyusi’s party claim the elections were free and fair. Nyusi was expected to come out victorious but not by such a large gap.
According to CNE, the country’s third largest party, Mozambique Democratic Movement represented by David Simango secured just over 4% of the vote with less than 1% going to Mario Albino who represented a smaller party, AMUSI.