Conservative National Action Party candidate Josefina Vazquez Mota - the first woman candidate for a major party in Mexico - conceded almost immediately, saying none of the exit polls favored her. Her party held the presidency for 12 years after kicking out Pena Nieto's Institutional Revolutionary Party in 2000.
The former mayor of Mexico City, Andres Manuel Lopez Obrador, said he would not concede defeat until all the votes were counted.
"We won't permit the new government to surrender to organized crime," Vazquez Mota told supporters as some yelled "the corrupt one won."
New Alliance candidate Gabriel Quadri, who trailed in single digits, also conceded, leaving Lopez Obrador as the single holdout. Lopez Obrador's narrow loss in Mexico's last election led to charges of voter fraud. This time, election officials insisted elaborate electoral machinery would make fraud almost impossible.
More than 79 million Mexicans were registered to vote in the election.
Pena Nieto, a 45-year-old former governor of the state of Mexico, has promised to crack down on the drug violence that has killed more than 50,000 Mexicans in recent years and create jobs.
"Hopefully we'll have a more stable neighbor," said UCLA professor Octavio Pescador. "Hopefully we'll have that confidence to travel and spend some time with our families in resort towns and cities in Mexico."