Ubuntu were relegated despite beating Eagles 1-0.
Eagles will now compete in the play-offs with Tshakhuma who finished third on the log.
Ubuntu were relegated alongside Witbank Spurs.
On the other hand, Stellenbosch FC were crowned the National First Division champions and they will be plying their trade in top flight football next season.
Eagles dominated the early exchanges with Sonke Ntuli and Mbulelo Wambi dictating terms with their swift passing.
Diego Brown was causing havoc for Ubuntu at the back with his physicality. He was playing as the focal point for Eagles.
The home side were gifted the lead after 15 minutes. Fawaaz Basadien profited from an exquisite cross from Wasim Isaacs. He dispossessed Samuel Manganyi who made a sloppy pass as he attempted to find Ntuli.
Eagles almost responded immediately but Lesvin Stoffels was denied by the woodwork. Eagles continued to pile on the pressure but their efforts were in vain as the home side went into the interval leading by a solitary strike.
Brown curled in a lovely free-kick but Azeemud-deen Bremer cleared the ball off the line.
Wambi also missed a sitter a few minutes before half-time. He was spotted by Ntuli but ballooned his effort over the bar and Ubuntu survived.
Ubuntu came back strongly in the second half as they closed the supply for Eagles from midfield. They were closing them down quickly and not allowing them to build from the back.
The visitors left a lot of open spaces in the second half as they pushed more numbers forward in search of the equaliser. Coach at Eagles, Sazi Ngubane, changed his tactics. He introduced Mario Booysen in the place of Diego Brown.@Minenhlecr7