Nene had fallen out of favour ahead of the coming season with the Team of Choice on his return from his loan spell last season from the now defunct Thanda Royal Zulu, who he helped to win the NFD title.
"We have managed to sign Mphakamiseni Nene from Maritzburg United and we have got him on a permanent deal," the club's general manager James Dlamini tells KickOff.com.
"He has already started training today and we are very happy, and the coach [Allan Freese] is very happy."
The 25-year-old Nene was influential for Roger Sikhakhane's AmaBhubesi last season as he featured in 28 league games.
Dlamini also confirmed that the club has also signed versatile player Nkanyiso Madonsela from Jomo Cosmos.
"We have also signed Nkanyiso Madonsela from Jomo Cosmos, who is the left-back and left-winger."
The duo add to the growing list of players signed by Eagles ahead of this coming season. The others include Cleopas Dube, Diego Brown, Bafana Nhlapo, Joshua Sauls, Dumisani Tau and Mazwi Mncube.