Maboke Matlakala decided matters with a smart finish in the 57th minute for the topflight strugglers, punishing some poor defending from Stuart Baxter's side.
SuperSport were the aggressors in the first stanza but few chances were carved out against a stubborn Bakgaga outfit.
The loss prevented United from claiming the summit and setting a new PSL unbeaten record, leaving them tied with Kaizer Chiefs.
Matsatsantsa are third on the table with 37 points from 21 matches - a point behind Bidvest Wits and two shy of Cape Town City.
Bakgaga - who ended a 15-game winless run in the league - remain at the foot of the standings with 18 points from 22 matches - a point behind Free State Stars and Bloemfontein Celtic.
Baroka's survival hopes were further bolstered as Highlands Park lost 2-1 to Golden Arrows in a simultaneous fixture.
The Lions of the North are 13th with 20 points from 22 games.