The results show a 6.62-percent victor for the Institutional Revolutionary Party candidate. Pena Nieto received 38.21 percent of the votes, while his closest rival, leftist Andres Manuel Lopez Obrador, got 31.59 percent.
Some are still challenging the legitimacy of the election, saying Pena Nieto engaged in vote buying. The accusations surfaces in June, but they climaxed this weekend when thousands of people rushed to grocery stores to redeem pre-paid gift cards that shoppers said were given to them by his party.
Simply giving away such gifts is not illegal under Mexican electoral law, as long as the expense is reported to electoral authorities.
The accusations are expected to become the basis of legal challenges to the final vote county, which must be certified in September by the Federal Electoral Tribunal. But the tribunal has declined to overturn previously contested elections, including a 2006 presidential vote that was far closer.
The official count included a recount of more than half of the ballot boxes.
The Associated Press contributed to this report.