The head of the AU team overseeing the poll, Olusegun Obasanjo, said turnout stood at between 30-35%.
He said some voters may have felt the result was a forgone conclusion and so abstained from casting a ballot.
President Omar al-Bashir is expected to extend his 25 years in power, after opposition parties boycotted the poll.
Voting in the presidential and parliamentary elections started on Monday and was extended until Thursday in a bid to boost turnout and enhance the legitimacy of President Bashir and his National Congress party.
The 71-year-old, who is wanted by the International Criminal Court on genocide charges, was virtually unopposed in the race.
He faced 13 minor challengers, after the main opposition parties pulled out, claiming the vote would not be free or fair.
Polling centres in the capital Khartoum were largely deserted, according to the Associated Press.
However, the party’s vice president Ibrahim Ghandour said the government was “quite satisfied” with the turnout.
Election results are expected on 27 April.