Van Heerden scored from the penalty spot late in the game as Roger Palmgren's side secured their second home win of the campaign.
The hosts threatened in the opening minutes, with Ayanda Dlamini's shot deflected wide.
However, AmaTuks got themselves into the game and created chances of their own, with Aubrey Ngoma shooting wide from outside the box in the eighth minute, before Mame Niang ballooned his shot over the bar a minute later.
Palmgren's men then launched attack after attack, but were unable to get past AmaTuks goalkeeper Washington Arubi.
The rain then started bucketing down in Umlazi, affecting the rhythm of the game and seeing the two sides going into the break goalless.
In the 56th minute Usuthu twice came close to opening the scoring with Teyise nudging the ball onto the post, while Ayanda Dlamini fired the rebound onto the crossbar.
In the 81st minute Usuthu were awarded a penalty when Tebogo Monyai was adjudged to have fouled substitute Goodman Dlamini inside the box.
Before the kick could be taken, the visitors were reduced to 10 men as Buhle Mkhwanazi got his marching orders after receiving his second booking. Van Heerden stepped up to take the spot-kick and made no mistake.
The hosts were able to hold on in the closing minutes to register their second win of the season, which sees them moving from the bottom of the log to 14th place.