Bafana Ba Gucci find themselves in sixth place on the league standings with 10 points from three wins, one draw and two losses.
They most recently drew 3-3 with Milford in their last league encounter and are next in action against the University of Pretoria at the weekend.
Mongoya only joined Upington at the start of the current campaign, from Kruger United after guiding the club to fifth place in their first ever National First Division campaign.
Speaking to KickOff, the coach confirmed the news. He said: "Yes, I have resigned.
"But this is not my place to talk about that, but the chairman’s. I am not a person of media, and please respect that."
Former Chippa United coach Vusumuzi Vilakazi has been given an immediate route back into management after being unveiled as the new head coach of Highbury FC ahead of the upcoming Motsepe Foundation Championship campaign.
Cape Town City have announced they have parted ways with coach Jan Vreman following their failure to gain promotion to the Betway Premiership via the play-offs.
Kruger United will play in the Betway Premiership next season after securing promotion from the Motsepe Foundation Championship as league winners with two matches still to play.
Baroka chairman Khurishi Mphahlele says he has no intention of buying a new status after suffering relegation from the Motsepe Foundation Championship.
