The Eastern Cape derby clash gave the team from NMMU their first goal of the season, after six rounds, courtesy of Simamkele Thobi.
But it was too late for the home side who remain bottom of the log after a goalless opening draw and four losses on the trot.
"It's a huge relief to finally have points on the board. A win would have been much sweeter but we'll take the draw," said Madibaz head coach Graeme Harrison.
"I'm proud of the boys. They really wanted to give the home fans a win, so they're disappointed about that, but they really played their hearts out."
After a sluggish start, which saw WSU's Mkhuseli Mfeketho score off a back-heel pass from Lutho Scotch in the 17th minute, the Madibaz regrouped and took the game to the opposition but were unable to finish with the required accuracy.
"We created so many opportunities but converting them into goals has been our problem throughout the competition," admitted Harrison.
However, his substitution of Chuma Mapuma for Sachin Jackson at left wing had immediate results when Mapuma gave the cross to Thobi who put the ball in the back of the net in the 61st minute.
"Chuma is a very exciting young player with a bright future ahead of him if he keeps his feet on the ground. Last night's performance showed what he's capable of."
Harrison said it was when the Madibaz stopped giving away possession and controlling the game in the second half that things came together.
"We had a chance again in the last minute of the game but their keeper made a brilliant save."
Madibaz centre midfielder Karabo Motlhabi, who missed four games due to a persistent ankle injury, was awarded the FNB Man of the Match prize for his efforts.
"He's inspiring – things happen on the field when he plays," said Harrison.
"We missed him throughout the campaign. His and striker Kieran Koert's injuries have not helped us this season."
The final match against log leaders UWC marks the end of the road for the Madibaz, who have also failed to qualify for next year's tournament.
"We haven't qualified because of the University Sport South Africa competition, where we finished fourth. They will only be taking the top three teams."
Harrison described his team, which included a large number of first-year students, as "a work in progress" and said their exit from the competition was possibly a blessing in disguise.
"We can now regroup and get our recruitment process in place so that we can come back stronger in 2017."
He promised to try and finish the season on a high note against UWC.
"We're definitely the underdogs but we want to send our fans home cheering with a victory at the end of the season.
"Their support meant a lot to us and we'd love them to come out again on Monday night."
The match kicks off at 5pm at the Madibaz Stadium.
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