John Antwi sent the home fans into wild jubilation after netting the opening goal in the 35th minute, with Eric Boateng providing the assist.
Boateng also set up Abdul Aziz Issah for the second goal 15 minutes from time.
Rivers United reduced the deficit through Alex Oyowah in stoppage time.
Club Africain secured the top position in Group C with six points from two games after defeating Academica do Lobito of Angola 3-1 away.
Rivers United dropped to second place with three points from the same number of matches.