Eagles took an early lead when Boikanyo Komane scored from the penalty spot. But AmaTuks staged a late come back as Chikohwa equalised with just over five minutes to the end, and completed his brace a few minutes later.
At Umthatha Stadium in the Eastern Cape, Mthatha Bucks had to settle for a share of the spoils as Humphrey Khoza equalised for Witbank Spurs a minute after Mpho Erasmus had put the home side ahead late in the match.
Tshakuma Tsha Madzivhandila scored their second win of the campaign springing a surprise on early season favourites Highlands Park handing them a 2-1 defeat.
Results: University of Pretoria 2 Royal Eagles 1; Mthatha Bucks 1 Witbank Spurs 1; Stellenbosch 2 Black Leopards 1; Super Eagles 2 Uthongathi FC 0; Real Kings 1 Ubuntu CT 1; Highlands Park 1 Tshakuma Tsha Madzivhandila 2.
Sunday Fixtures: Jomo Cosmos v Richards Bay FC at Vosloorus Stadium; Cape Town All Stars v Mbombela United.