"I thank all Guatemalans who trusted in me," the ex-general said on local radio Sonora, as he was set to become the first military man to lead Guatemala since the end of army rule 25 years ago.
"I call on all Guatemalans who didn't vote for Otto Perez to unite to work together for the next four years."
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Perez won 54.5 percent of the vote against 45.5 percent for populist businessman Manuel Baldizon, according to 96 percent counted by the Supreme Electoral Tribunal, just hours after the close.
Although the lush Central American nation, famed for its Mayan ruins, has vast social problems -- with more than half the population of 14 million living in poverty -- the campaign was dominated by the issue of insecurity and growing drug violence.
Brutal attacks from Mexico's Zetas drug gang have joined lingering political attacks in the country still struggling to emerge from a 36-year civil war, which ended 15 years ago.
Despite that painful history, the 61-year-old ex-general convinced voters he was best placed to reduce a murder rate of 18 per day, six times the world average.
"We're going to fight very hard to bring peace, security, work opportunities and rural development," Perez said Sunday, four years after narrowly losing to current President Alvaro Colom.
Perez focused his campaign for the Patriotic Party (PP) on creating jobs and cracking down on crime, proposing to use the army against drug traffickers.
Baldizon, a 41-year-old from the Renewed Democratic Liberty (LIDER) party, promised to increase use of the death penalty, including on television.
Experts said the tough stance of both candidates underlined concerns about security, but they criticized the lack of concrete proposals to reduce poverty.
"They talk about it in generalized terms, but they haven't said how they'll tackle or reduce it and that's worrying," said indigenous political analyst Alvaro Pop.
Amid a typically tense electoral climate, the two candidates traded insults Sunday, with Perez accusing Baldizon of offering roofing and food in exchange for votes, and Baldizon repeating accusations of rights violations under Perez during the civil war.
Perez -- who represented the army to sign peace accords in 1996 -- has denied accusations that rights abuses took place under his command during the war, in which some 200,000 people are believed to have died or gone missing.
Perez will take over from center left President Alvaro Colom on January 14, after losing to him in a runoff last time around.
Colom, who is limited to a single term, managed to break a half-century of domination by the hard right but struggled to reform the Central American nation with limited means and a fragile majority.
His National Unity of Hope (UNE) party failed to present a candidate because his wife, Sandra Torres -- who filed for divorce to try to run for office legally -- was disqualified.
Perez and Baldizon spent $22.5 million and $13.7 million respectively on campaigning for the September first round -- in a country where two million people survive on less than a dollar a day.
Around 98 percent of crimes go unpunished in Guatemala, according to the United Nations, while malnutrition affects 49 percent of minors and 30 percent of the population is illiterate.
The treasury is also bankrupt after right-wing opposition parties blocked current government attempts at fiscal reform and the approval of 500 million dollars in loans.
Perez also faces tough political deals in Congress, holding only 54 of 158 seats.
For the first time, a woman, Roxana Baldetti, is set to become Guatemala's vice president.
