Luke Ivanovic cancelled out Dylan Wenzel-Halls early strike for Brisbane in a high-tempo encounter played behind closed doors in Newcastle.
A second 1-1 draw in succession means Sydney FC are now winless in four matches, a run not endured by the club since early 2016.
Brisbane Roar missed an opportunity to end the season in third, in a match in which both teams will lament missed opportunities.
Sky Blues' coach Steve Corica opted to leave out his two most experienced players in captain Alex Wilkinson and creative maestro Milos Ninkovic, although the pair's absence was partly offset by the return of midfielder Luke Brattan and attacker Kosta Barbarouses.
Brisbane Roar went into the contest with just one defeat from their past six matches, while Sydney FC conversely had managed just one win in their past six outings.
Dylan Wenzel-Halls opened the scoring with a composed clipped finish past an exposed Andrew Redmayne after just 11 minutes, having latched onto a pass in behind a static defence.
The lively Wenzel-Halls continued to cause problems, while Jay O'Shea flashed a freekick just wide as the Roar dominated goalscoring opportunities, if not possession.
Sydney FC lined up with four under-23 players in their starting side and it was one of the young brigade who helped turn the tide.
Ivanovic equalised with an even better strike, curling a shot into the far corner after creating space in the penalty area.
The 20-year-old, however, was replaced at halftime by Ninkovic who immediately started to make an impact.
The former Serbian international soon forced a couple of saves from goalkeeper Jamie Young as did Brattan.
Young then displayed part of the reason for the Roar's remarkable defensive record in the second half of the season, with their goal breached just eight times in the past 13 matches.
The Brisbane No.1 pulled off a miraculous block as the clock wound down to deny Alex Baumjohann twice in a matter of moments as the Roar goal lived a charmed life.
The Roar carved plenty of their own sights of goal at the other end with notably Danny Kim and Jack Hingert having a chance to find a winner.
Sydney FC will conclude their regular season campaign on Saturday against Western United when they will be presented with the premiership trophy.
