Matsatsantsa a Pitori fell to a 2-1 defeat to Amakhosi after William Twala banged home a late winner for the home side at Cape Town Stadium.
Chiefs opened the scoring through George Maluleka but Jeremy Brockie volleyed home the equaliser 11 minutes later, before Twala latched onto September's flick-on inside the United box in the 88th minute.
However, the 33-year-old experienced defender looked to have been fouled by Mathoho while trying to head clear Daniel Cardoso's initial throw-in, and admitted that the Bafana Bafana defender had "nudged" him in the back.
"We had order in terms of the second goal ... the referee's decision is final after all, so maybe I could have been stronger to head the ball forward but I believe it was a foul," September told SuperSport after the match.
"I judged the ball well, I thought it was going to drop on me, and I could feel him [Mathoho] behind me just when I was about to jump, and I felt the nudge.
"Maybe I could have been strong, but I felt the nudge and it's one of those."
The result is Stuart Baxter's side's second defeat in three matches as they now drop to 10th place on the log, with 24 points from 20 games.