Collins Mbesuma bagged the only goal of the match as The Lions of the North claimed three points for the first time in seven matches.
The delayed start and the wet, cold weather conditions seemed to have an effect on the game as the first half ended goalless with chances coming few and far between.
Muzi Thabota forced Daniel Akpeyi into a good save to his right with a powerful right-footed shot from 18-yards out just before the hour-mark.
The hosts went into the lead in the 65th minute as Mbesuma converted a penalty, after Seun Ledwaba was brought down inside the Chippa box under a slight touch from Justice Tshabalala.
Peter Shalulile should have doubled his side's advantage in the 70th minute as he did well to get onto the end of a ball behind the Chippa defence, but his shot was disappointing as he failed to test Akpeyi with a wide attempt.
Highlands held on to see out the encounter as the Chilli Boys threw the kitchen sink and the dishes at Marlon Heugh's goal.
The Tembisa-based outfit have now moved into 14th place, trading places with Chippa, who drop into 15th place and level on points with bottom side Baroka, who will play their game in hand against Golden Arrows on Saturday.