Ekenne Awazie gave Enyimba the lead six minutes before the break after Enyimba failed to clear their lines.
Rivers United fought back and got the equaliser through Nyima Nwagua three minutes after the break.
Enyimba will also compete in the CAF Champions League next season.
Remo Stars came second with same points but have an inferior goal difference.
The Sky Blue Stars will compete in the CAF Champions League for the first time.
Rivers United finished in third position and earn a secure a berth in the CAF Confederation Cup.