Pena Nieto, 45, a telegenic former governor of the Institutional Revolutionary Party, or PRI -- which ruled the country under different names for 71 years, until 2000 -- defeated leftist Andres Manuel Lopez Obrador, his closest rival, with about 38 percent of the vote to 31 percent, the autonomous Federal Electoral Institute reported late Sunday.
In his victory speech, Pena Nieto stressed the need to end political polarization and keep government transparent.
"We will build the results-driven democracy that Mexicans deserve, starting with an effective, honest, transparent and accountable government -- a government that fights corruption head-on ... a government that strictly observes and ensures the rule of law," he said.
U.S. President Obama called Pena Nieto to congratulate him on his victory, the White House said.
"The two leaders reaffirmed the close bilateral partnership the United States and Mexico enjoy based on mutual respect, shared responsibility, and the deep connections between our people," the readout released by the White House said.
Obama also reiterated his commitment to working with Mexico and said he looked forward to the two countries advancing common goals such as promoting democracy, economic prosperity and security in the region and globally.
"The president also congratulated the Mexican people who have once again demonstrated their commitment to democratic values through a free, fair and transparent election process," the readout said.
Pena Nieto appointed Gen. Oscar Naranjo, a retired Colombian police chief, to serve as an adviser on crime-fighting measures, with an emphasis on strengthening enforcement and improving cooperation with other countries.
"The fight against crime will continue -- yes, with a new strategy to reduce violence and protect, above all, the lives of Mexicans," Pena Nieto said. "In the face of organized crime, there will be neither negotiation nor truce."
Conservative candidate Josefina Vazquez Mota, 51, of the currently ruling National Action Party, or PAN, conceded in a televised speech. She was Mexico's first major female candidate and garnered about 26 percent of the vote, said the institute, which based its reports on a quick count of 7,500 voting locations.
PAN held the presidency for a dozen years after defeating the PRI in 2000.
Lopez Obrador, a populist former Mexico City mayor of the left-leaning Party of the Democratic Revolution, or PRD, refused to accept defeat, saying he would wait for the final results.
In 2006, when Lopez Obrador last ran for president, he alleged widespread fraud had led to Felipe Calderon's narrow victory over him, and he launched months of street protests.
Calderon, who was elected to a single six-year term, was constitutionally barred from seeking re-election.