The head of the Election Commission, Mokhtar al-Assam, announced the results to reporters. He said turnout was 46.4 percent, insisting that widespread reports of low participation were "not accurate."
He said al-Bashir won 5.58 million votes. The other 12 presidential candidates were virtually unknown to the public.
The four-day vote began April 13. Nearly 13 million people were registered to vote at some 11,000 polling centers. Polling stations in the capital, Khartoum, were largely deserted.
Al-Bashir, who took power in a bloodless Islamist coup in 1989, is the only sitting head of state facing genocide charges at the International Criminal Court. The charges stem from the conflict in Darfur, where 300,000 people were killed and 2 million displaced during the government's brutal response to an armed rebellion.
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The Sudanese opposition boycotted the vote after the government refused to postpone elections until a national unity government could be formed to ensure their fairness.
In a joint statement released Sunday, the opposition said it will not recognize the election results. It called upon the Sudanese people to join ranks to "topple" al-Bashir.
The vote was the second multi-candidate election to be held in Sudan since al-Bashir came to power.
The election generated little excitement in Sudan, but was not entirely insignificant.
Al-Bashir must remain in office to ensure he is never sent to the Hague to face the war crimes charges, and needs at least the veneer of legitimacy to attract badly needed foreign aid and investment after the 2011 secession of oil-rich South Sudan.