Givemore Khupe scored the winning goal from penalty spot to steer his side to 13 points in fourth place, from their opening seven games of the new Motsepe Foundation Championship season.
Nyatama claimed the hotseat from Abram Mongoya having coached Leruma United last season, alongside a spell as Chippa United as assistant coach.
Speaking after the weekend's win, the coach said on Soccer Laduma: "To be honest with you, this is a team that has got potential.
"You can see the level of experience and they have youngsters who are willing to work. So, I saw the team has potential and why not give it chance?"
"It feels good (to get the win), but I don't think we should get carried away. I should be humble and tell my players to be humble.
"I started on Thursday with the boys, so it was two days before the game, but the foundation that was laid was good. We have a good bunch of players who are willing to work for each other," the coach added.
Upington take on Baroka in their next league game on Tuesday.
The Nedbank Cup Round of 16 delivered high drama as TS Galaxy stunned Mamelodi Sundowns with a clinical 2-0 win, while Durban City held their nerve to knock out Upington City on penalties after a gruelling stalemate.
University of Pretoria head coach Kwanele Kopo says AmaTuks' rich history in developing top players and competing strongly in the Nedbank Cup is central to his vision as the club looks to make a deep run in this season's competition.
Former Kaizer Chiefs midfielder Kgaogelo Sekgota is embracing a new chapter in his life and career after completing a four-month rehabilitation programme at the Hope of Achievers Rehabilitation Centre outside Polokwane.
Upington City have announced the appointment of Musa Nyatama as their new head coach.
