Nhlanhla Gasa broke the deadlock at the King Zwelithini Stadium on Wednesday in the 76th minute, but they held their lead for just two minutes before Genino Palace netted an equaliser.
Arrows ended the evening in eighth place on the league standings with 25 points from 21 games, with Stellenbosch in 10th, also with 25 points.
Speaking after the game, Mngqithi explained that his team performed well below their best and conceded a "silly" goal before improving slightly with a number of changes in the second half.
"Our first half lacked mobility and didn't really show much, but our second-half performance was strong. We showed intent," Mngqithi said in the Post.
"The substitutions came on and really gave a good account of themselves. Unfortunately, we conceded such a silly goal from our own mistake because we kept playing the long ball. We couldn't really control the game after scoring and that's why we conceded
“We never really supported (Junior) Dion up front in the first half,” Mngqithi added. "Everyone wanted the ball at their feet and they never tried to move into the spaces they gave us.
"Their centre-backs were following our strikers, so there were spaces in between. But there was no movement in the first half. But the boys who came in during the second half really gave us what we wanted."