His rival Domingos Simoes Pereira, head of the country’s historic ruling party PAIGC, took 46.45 percent in Sunday’s runoff.
“I declare Umaro Sissoco Embalo to be the winner of this second round,” CNE President Jose Pedro Sambu said.
Embalo supporters erupted with joy close to the tightly-policed hotel in the capital Bissau where the results were announced.
They beat pots and cans and sang and danced. Some bore giant red-and-white keffiyehs, the Arab headdress that became Embalo’s campaign trademark.
Embalo, 47, takes over from Jose Mario Vaz, who came to power in 2014 on hopes of stabilising a country notorious for coups since gaining independence from Portugal in 1974.
But his tenure was hampered by a paralysing faceoff with parliament under the country’s semi-presidential political system.
The CNE put turnout at 72.67 percent, virtually identical to the first round of voting on November 24, which Pereira won with 40.1 percent against 28 percent for Embalo.
Embalo is nicknamed “The General,” a reference to his rank as a reserve brigadier general. He quit the army in the 1990s.
Like Pereira, he is also a former prime minister, serving under Vaz between 2016 and 2018, before representing Madem, a party formed by PAIGC rebels.
He fought to overcome his first-round vote deficit by portraying himself as a unifier of the country and by gaining the backing of eliminated candidates, including Vaz.
Elisa Pinto, an election monitor representing Guinea-Bissau civil society, said the vote had proceeded smoothly and there was a clear result.
“The election went off well. One candidate won,” she told AFP.
But, she added, “he will have a lot of responsibilities at these difficult times… (he) will have to address the public’s concern, and the public needs stability and national reconciliation.”
“Without that, there cannot be development,” Pinto warned.
Embalo’s prime task will be to deal with a legislature dominated by the PAIGC — the African Party for the Independence of Guinea and Cape Verde (PAIGC), which led an 11-year armed struggle to end Portugal’s colonial rule.
Under the constitution, the parliament has the right to designate the prime minister, but this appointee can be fired by the president — a circular problem that led to the paralysis during Vaz’s presidency.
Poverty, graft and coups
Nearly 70 percent of Guinea-Bissau’s 1.8 million people live on less than $1.90 (1.69 euros) a day.
The country ranks 178th out of 189 on the UN’s Human Development Index. Average life expectancy is just 57.8 years.
Latin American drug runners have exploited the instability and poverty to make the country a hub along the cocaine-smuggling route to Europe.
It also has a notorious image for graft. It was placed 172nd out of 180 countries in Transparency International’s 2018 index for perceived levels of corruption.
Since independence, Guinea-Bissau has been through four coups as well as 16 attempted, plotted or alleged coups.
After the last coup, in 2012, the regional bloc ECOWAS sent a stabilisation force comprising more than 700 troops and police.
Armed forces chief General Biague Na Ntam repeatedly declared during the latest election campaign that the military would not intervene.
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