Ramahlwe Mphahlele scored in second-half stoppage time to secure all three points for Downs, who finish the season in second spot on the log standings. AmaTuks finished the game with 10 men after Grant Kekana received his marching orders for a challenge on Rodney Ramagalela in the 84th minute.
Chasing a favourable finish in the log standings, AmaTuks came out guns blazing, with youthful pair Thabo Mnyamne and Botshelo Mfulwane going close for the visitors in the opening exchanges.
Mnyamane directed his free-kick straight at Thela Ngobeni before Mfulwane sent his effort wide, having been put straight through in the sixth minute.
Pitso Mosimane made no fewer than seven changes to the side that beat SuperSport United in midweek and it showed as they struggled to find their rhythm.
Anthony Laffor and Mame Niang fired speculative efforts at Lebogang Ngubeni 's goal, but nothing to work the AmaTuks keeper who was hardly tested in the first-half.
Downs dominated the closing exchanges, but a combination of over-playing and good defending by the visitors kept out the Brazilians as the teams headed for the break deadlocked.
Ngubeni was forced into action two minutes following the interval. The AmaTuks gloves man made a courageous stop to deny a sliding Mphahlele at the back post.
Downs turned up the pressure with Laffor again in the thick of things, the Liberian, though, saw his powerful effort go straight at Ngubeni in the 55th minute.
Grant Kekana saw red with six minutes of regulation time remaining before Mphahlele popped up to score the winner in the 91st minute.
The former AmaTuks fullback lost his marker before heading Laffor's corner-kick into the roof of the net to condemn AmaTuks to a 13th place finish.