SuperSport suffered a late blow with Kingston Nkhatha sent off for the second time this season, but Matsatsantsa held firm to secure only their third victory of the season.
Ajax slip to 12th with their winless run in the League stretching to five games.
Phala raced onto a Jeremy Brockie through-ball in the fifth minute before chipping the onrushing Anssi Jaakkola to hand Matsatsanta an early lead.
The goal set Ajax into motion with the Urban Warriors pressing for the equaliser. Toriq Losper saw his first shot fly wide, but did force Ronwen Williams into a smart save on the cusp of half-time.
Ajax though had to be on their toes with SuperSport dangerous on the counter and were it not for a timely interception from Abbubaker Mobara the Urban Warriors would've gone into the break two goals behind.
Nkhatha saw red for a second bookable offence – rolling the ball away from Jaakkola after an offside call – in the 73rd minute before Frankin Cale saw his chip come back off the crossbar a few minutes later.
This would be the closest the Urban Warriors would come to an equaliser as SuperSport held on for all three points.