The Independent National Electoral Commission reported Yar'Adua won 24.6 million votes, about four times the number of votes won by the strongest opposition candidate, Muhammadu Buhari of the All Nigeria People's Party.
At least 200 people died during polling over the weekend, and election observers reported ballot stuffing, shortages of voting papers, ballot box snatching and underage voting, among other election violations.
The Transition Monitoring Group, a Nigerian democracy organization with 10,000 election monitors, said the election effectively never occurred in 13 of the 36 states, reported the Washington Post.
Yar'Adua was backed by President Olusegun Obasanjo, who acknowledged weaknesses in the election process during a nationwide address Monday and accused some political leaders of encouraging political violence.
International criticism of the election has been widespread, and chief EU observer Max van den Berg said the polls did not meet international standards.
"The elections have not lived up to the hopes and expectations of the Nigerian people, and the process cannot be considered to be credible," he said.
The United States responded with concern to the announcement of Yar'Adua's victory.
"These were flawed elections and in some cases deeply flawed elections," said State Department spokesman Sean McCormack.
However, the United States is not calling for another election, McCormack said.
Opposition candidates, including Vice President Atiku Abubakar, have demanded a new election and called the polling a sham.
Abubakar was at the center of a dispute between the Nigerian court system and the electoral commission in the run up to the election. He was banned from running by the electoral commission and then reinstated just days before the election by the Nigerian courts.
Obasanjo encouraged parties to use legal avenues for any grievances until the new president takes power on May 29.
"My hope is that by the time the election tribunals and appellate courts complete the review of the cases before them, Nigerians will reconcile with one another and the nation will move on," he said.