The official tally found Pena Nieto, of the Institutional Revolutionary Party, ahead of runner-up Andres Manuel Lopez Obrador by 6.6 percentage points.
"I am president by the majority decision of the Mexicans," Pena Nieto told CNN.
Lopez Obrador, of the leftist Party of the Democratic Revolution, said he intends to challenge the results and alleged the PRI bought votes.
In the 2006 election, Lopez Obrador made claims of election fraud when he lost to Felipe Calderon by a narrow margin. He never conceded and referred to himself as "the legitimate president of Mexico."
In the recent election, PRI opponents allege they have video and photo evidence of the party buying votes through handing out gift cards to a chain of supermarkets.
Election officials said they were investigating those allegations.