Midfielder Abuaagla Abdalla put the Sudanese ahead on 48 minutes and Mohamed Abdelrahman doubled the advantage with 15 minutes remaining.
The match pitted two French coaches against each other with Hubert Velud in charge of Sudan and Emmanuel Tregoat guiding Chad.
Sudan scored two late goals to win 3-2 in midweek as both teams prepare for the resumption of 2021 Africa Cup of Nations qualifying, which has been delayed by the coronavirus pandemic.
The Sudanese have arranged two more friendlies next month, against Tunisia and Togo, before facing Cup of Nations Group C frontrunners Ghana twice between November 9 and 17.
During the same window, Chad will tackle Group A table-toppers Guinea at home and away as they seek a first appearance at the Cup of Nations finals.