Mr Cartes is a newcomer to politics, who only joined the Colorado Party in 2009.
During his campaign, Mr Cartes had to confront accusations of fraud and links with drug trafficking.
In his victory speech, Mr Cartes said that that he would lead Paraguay in "a new direction".
He named Horacio Cartes, a would-be Colorado presidential candidate, as the leader of a conspiracy against him.
ECONOMIST: Paraguay��s impeachment: Lugo out in the cold | The
Paraguay's President-elect Horacio Cartes, a wealthy businessman, has said he would "never put personal interests before the country's".
Voters said they had been swayed by Mr Cartes' campaign promise to raise private capital to fund infrastructure and modernise state-owned companies.
Mr Cartes said he would make rejoining them one of his priorities.
With tears in his eyes and the Paraguayan flag wrapped around his neck, Mr Cartes said he would be the president of all Paraguayans.
After his election win was declared, Mr Cartes called on all Paraguayans, regardless of their political affiliation, to "work together" to reduce Paraguay's rampant poverty.
Mr Cartes, one of Paraguay's richest men, told reporters there would not be conflict of interest as he governed one of South America's poorest nations.
Many also voiced their hope that Mr Cartes, who is well connected with Paraguay's wealthy landowners and agricultural businesses, would create employment and draw international investment.
Mr Cartes said he relinquished the control of his enterprises, including a bank, Paraguay's largest tobacco company and a variety of agricultural businesses, to his sister, Sarah.
But after Sunday's elections, leaders of the other co-founders of Mercosur, Brazil, Argentina and Uruguay, called Mr Cartes to congratulate him and left the doors to the bloc open.
He tried not to travel much, did not take holidays, and if the journey was unavoidable made what he called cartes de voyage, continuing his numbers in black ink on ordinary white paper.
Mr Cartes, a businessman, is a controversial figure.
ECONOMIST: Paraguay��s impeachment: Lugo out in the cold | The
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