The Leopards made a flying start when Wissa opened the scoring in the fourth minute, converting Nathanal Mbuku's assist.
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Samuel Moutoussamy doubled the hosts' advantage in the 35th minute, ensuring Sebastien Desabre's side entered the break firmly in control.
DR Congo continued their dominance after the restart, with Edo Kayembe extending their lead in the 58th minute following Arthur Masuaku's assist.
Sierra Leone grabbed a consolation through substitute Stephen Bekoe seven minutes from time but could not prevent defeat.
The victory leaves DR Congo top of Group E with nine points from three matches.
Both teams meet again on November 17, with the Leopards seeking another victory to strengthen their qualification hopes.