In the second match, a Group A tie hosts Uganda and Tanzania settled for a 1-1 draw.
Saleh Ally gave Tanzania the lead after 19 minutes, but Uganda piled pressure and leveled matters after 58 minutes through Isima Magala.
South Sudan now top Group B with three points and will next face Sudan in their second match.
Action will continue on Wednesday with Tanzania facing Kenya in a Group A tie, while South Sudan take on Sudan in a Group B match.
The best two teams will qualify for the U-17 AFCON to take place in Ivory Coast next year.