Kamogelo Sebelebele scored the only goal of the game at the Mbombela Stadium on 44 minutes, to steer his side into fourth place on the league standings with 25 points from 17 games.
Sundowns saw their ten game winning streak come to an end but remained top of the standings with 42 points, from 16 games, nine clear of Orlando Pirates in second place.
The home side, meanwhile, extended their unbeaten run to 12 games. They came into this game on the back of a 1-0 win over Chippa United, and started well as they pressed their opponents aggressively, and leaving little space to play.
Lucas Ribeiro was eventually able to find some room to get away a snapshot from a Tashreeq Matthews pass, but he was denied by a post.
Ronwen Williams was then forced to make a fingertip save at the other end following a rasping shot from the edge of the area from Sphiwe Mahlangu.
Both sides battled for supremacy, but it was the Rockets who found a breakthrough, a minute before half-time as Sebelebele toe-poked the ball past an onrushing Williams after a neat ball to the near post from Dzenan Zajmovic.
Matthews made way for Iqraam Rayners at the start of the second half and Thapelo Morena was introduced for Kegan Johannes.
Chances remained few and far between after the break, with Teboho Mokoena coming as close to anyone as scoring with a blasted free-kick that Rockets stopper Ira Tape somehow managed to keep out.
Mokoena's second attempt as a free-kick was punched clear by Tape before Modiba skied the rebound for what proved to be the last real chance of the game, as Sundowns slumped to just their second defeat of the season, and first under head coach Miguel Cardoso.
Former Kaizer Chiefs winger Joseph Malongoane has urged Amakhosi supporters to remain patient with co-coaches Khalil Ben Youssef and Cedric Kaze, arguing that the pair needs time to understand the unique demands of South African football.
Kaizer Chiefs co-coach Khalil Ben Youssef has admitted his side continues to struggle in front of goal but insists the team is working hard to solve the problem ahead of Sunday’s clash with TS Galaxy in Mbombela.
Orlando Pirates captain Nkosinathi Sibisi is keeping his focus sharply on the Carling Knockout Cup title as his team tops the Betway Premiership table with 28 points after 12 games.
Golden Arrows head coach Manqoba Mngqithi has praised a select few PSL teams for their progressive style of play while criticising the majority for adopting what he calls "negative football."
