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Morales, a comic actor and TV personality with no political experience, had 69% of the vote to 31% for former first lady Sandra Torres, with 94% of polling stations reporting.
“With this election you have made me president, I received a mandate and that mandate is to fight the corruption that has consumed us,” said Morales on national TV.
“Thank you for this vote of confidence. My commitment remains to God and the Guatemalan people, and I will work with all my heart and strength not to defraud you.”
Torres conceded defeat in a brief televised address, telling Guatemalans that “the people have made their choice and we respect it. We wish Mr Morales the best of success.”
It has been a remarkable ride for the conservative candidate, who started the race with just 0.5% support back in April.
The campaign was rocked by president Otto Perez’s resignation and arrest on corruption charges on September 3, three days before the first-round vote.
Perez, who is in jail awaiting trial, is accused of masterminding a corrupt network of politicians and customs officials that took bribes from businesses in exchange for illegal discounts on import duties.
Prosecutors and United Nations investigators say the network collected $3.8m in bribes between May 2014 and April 2015 — including $800 000 each to Perez and jailed ex-vice president Roxana Baldetti.
Morales rode a wave of outrage with politics-as-usual in the impoverished Central American country, which is torn by gang violence and still recovering from a 36-year civil war that ended in 1996.
He won the first-round vote with 24% to 20% for Social Democrat Torres.
Clinic with no medicine
Morales, 46, is famous for playing a country bumpkin cowboy who nearly becomes president in the 2007 film “A President in a Sombrero.”
In real life, the presidential race was his first foray into national politics, though he once ran unsuccessfully for mayor of his hometown.
Morales will be tasked with rebuilding confidence in the government at a time of deep public distrust, shaky institutions and a depleted treasury.
“The new president will face a sombre panorama because the state is in a death spiral,” said Manfredo Marroquin, head of the local chapter of Transparency International.
Morales will also have to govern with just 11 seats in the 158-seat Congress.
Voters voiced concern about the political situation as they cast their ballots.
“Politically, Guatemala is still in diapers and I’m worried,” said architect Monica Figueroa.
Textile salesperson Francisco Estrada agreed “things are really bad.”
“The next president must at least purge the police and clean up the government,” he said.
In the central town of Chinautla, whose mayor is in jail awaiting trial for money laundering, 35-year-old Leocadio Lic bemoaned rampant corruption.
“Here we have a health centre, but the sad thing is it has no medicine because of corruption,” he told AFP.
