Despite the loss at Tuks Stadium, Chippa stay sixth on the log.
The victory sees Shaun Bartlett claim his first win as head coach of the Pretoria side.
For AmaTuks, the three points move them to within a point of Jomo Cosmos in 15th place and four points clear of bottom-placed Maritzburg United.
Willem Mwedihanga, Thabo Mosadi and Getaneh Kebede got their names on the score sheet for the hosts, who registered their fourth win of the season.
Meanwhile, Bloemfontein Celtic owner Max Tshabalala caused a sensation in PSL circles by announcing he was courting offers for the team after fan violence at their PSL clash against Orlando Pirates on Saturday.
There has been growing anger towards Tshabalala from Celtic supporters after the chairman accused them of “barbarism”.
The side have achieved just a single victory in their last 16 matches in all competitions.
They went down 1-0 on Saturday, sparking a rampage at the Orlando Stadium where they ripped up seats and attacked rival supporters.
Hour later, Tshabalala said he wanted out of the club.