The Gauteng champions, who together with Rovers won promotion into the National First Division, played a tight game until Orlando Pirates development graduate Kyle Koert, grabbed the winner with seven minutes to go.
Earlier, his teammate Leroy Plaaitjies opened the scoring in the 14th minute, but a spate of second half goals had the fans on the edge of their seats, especially when Rovers leveled matters in the 65th minute through Lebohang Mpapea's magnificent long-range shot.
Five minutes later, Richard Danse grabbed FC AK's second goal but the celebrations lasted only just sixty seconds before Rovers equalized through Thandolwethu Prins.
After the game, Safa CEO Leslie Sedibe told the media, "We witnessed one of the most entertaining finals this afternoon and I congratulate the teams for the tenacity they showed over the past week and showcasing some of South Africa's talent at this high level.
"The plan is produce enough quality that the teams in the Vodacom Second Division can emulate Mapate Silver Stars (now Platinum Stars) and Vasco da Gama, who were crowned the Vodacom league champions in 1999 and 2008, respectively, then gained promotion to the PSL after winning the First Division."
He also thanked the communities of Mhluzi and eMalahleni for supporting the Play-offs.