Nigeria had picked up just one point from their opening three games in Group A but the home win ensured they are now back in the race for a place at the finals in Morocco in January -- although they will probably have to win their last two qualifiers next month to make sure.
Musa opened the scoring after a mazy run on goal just after halftime but Sudan equalised eight minutes later through Ibrahim Salah.
Giant striker Aaron Samuel, making only his second appearance, bundled the ball over the line to restore Nigeria's lead in the 66th minute and Russian-based winger Musa made sure of the win three minutes from the end of a match played for a large part in heavy rain.
(Reporting by Mark Gleeson in Johannesburg; Editing by Neville Dalton)
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