Bashir, who is wanted by the International Criminal Court on war crimes charges, faced little competition in the four-day vote with just 13 little-known challengers standing against him.
The mainstream opposition boycotted the polls and called on voters to stay away, saying conditions were not right for a free and fair election.
Polling stations were quiet during the vote, despite a nationwide one-day extension, and the African Union’s Election Observer Mission said there had been a “generally low turnout of voters throughout”.
The controversial vote has already faced international criticism, with the US, Britain and Norway slamming Sudan last week for its “failure to create a free, fair and conducive elections environment.”
If no candidate for the presidency wins an outright majority, the electoral law requires a second-round runoff.