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."
Black Leopards find themselves in a difficult position, unable to register new players due to a debt inherited from All Stars FC when they purchased their Motsepe Foundation Championship status in 2023.
Motsepe Foundation Championship side University of Pretoria have announced a massive overhaul of their squad with 18 new signings.
Venda FC have rung the changes ahead of the new Motsepe Foundation Championship season, unveiling 13 new players as they look to turn the page on last year's relegation scare.
Motsepe Foundation Championship side Cape Town City have snapped up former Mamelodi Sundowns defender Sifiso Ngobeni.
