The announcement follows disputes about the validity of the vote by President Joyce Banda.
A crowd celebrated outside the tally centre in the commercial hub of Blantyre as Mutharika was announced on Friday as the winner of the disputed elections with 36.4 percent of the vote.
Banda, southern Africa's first female president, trailed in third place with 20.2 percent of the vote.
Mutharika, 74, is the brother of the late President Bingu wa Mutharika and was leading the results on May 24 when Banda ordered the parliamentary and presidential elections cancelled, citing "rampant irregularities". Malawi's High Court issued an injunction the same day, stopping Banda from interfering with the vote.
Second place went to Lazarus Chakwera of the Malawi Congress Party with 27.8 percent of the vote.
"We have to now focus on what matters. Spend our tax money wisely ... What unites us Malawians is more important than what divides us," Malawi Electoral Commission Chairman Maxon Mbandera said to Mutharika.
Three people have been killed in violence following the vote. One was shot dead on Friday by police when they clashed with protesters demanding a recount.