The Port Harcourt club started the day in second place and knew they had to win to guarantee themselves a place on the continent.
Obomate Frederick and Guy Kuemian scored for Rivers United either side of half time while Fortune Omoniwari claimed the consolation for the visitors.
After the tension-soaked game, a relieved Rivers technical United manager, Stanley Eguma spoke about a difficult season which ended in positive fashion for the club.
“We suffered a lot but I thank God that we have been vindicated in the end.
“This club came into existence just days before the season commenced and we were a lot of people’s favourites to be relegated.
“We however knew what we were about and stood true to our values of hard work, discipline and total trust in God.
“Today, the result is there for all to see.
“To have gone into the final day (of the season) still with a chance to win the league is no mean feat.
“It is a pity we did not win the league title but it is quite clear that we performed much better than a lot of people thought we would,” he told Rivers United Media.
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