It was the sixth goal the bottom-placed visitors had conceded this season after the 90th minute.
United conceded two goals in added time on Tuesday night in the 2-1 loss to Melbourne Victory.
It was veteran defender Corey Brown who sent in the cross for Markovski to pounce.
The draw kept the Roar in eighth place on the ladder, just three points behind sixth-placed Western Sydney but they have played two more games.
Jonas Markovski at the death 💪— Brisbane Roar FC (@brisbaneroar) #BRIvWUN | 🎥 @10FootballAU pic.twitter.com/YOLwZBDnJZFebruary 23, 2024
In action for the third time in eight days, Western United made the dream start.
In the sixth minute Brisbane defender Antonee Burke-Gilroy failed to clear a cross and Nikita Rukavytsya pounced to score.
The Roar played with a lack of intensity in the opening half compared to their last home game against Melbourne City when they were full of running in a 5-1 win.
It was a sluggish start that proved very costly.
Brisbane had few opportunities in the first half. Striker Tom Waddingham had three half-chances while a header at the far post from unmarked defender Tom Aldred was defended by Western, drawing unsuccessful appeals for a handball from the home side.
Roar's Keegan Jelacic and Aldred had a headers negotiated by fingertip saves by Matt Sutton in a matter of minutes after the break.
Sutton wasn't able to save a third when Waddingham headed home in the 58th minute from a Florin Berenguer corner for his fifth goal of the season.
It was 18-year-old Waddingham's fourth in three games.
The goal gave the visitors a wakeup call after they had tried to defend their lead.
Western United's Riku Danzaki sent an inch perfect cross in for Noah Botic to shrug off Waddingham and score in the 79th minute.
Markovski then earned a point for the hosts.
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