Roar opened proceedings when youngster Matthew Dench scored on his A-League Men debut in the 48th minute, after kick-off was delayed by an hour because of lightning near a rain-soaked Campbelltown Stadium.
The Bulls were dealt a further blow on Friday night when Tomi Uskok was ruled out with concussion in the 63rd minute.
But a penalty conceded by Brisbane centre-back Lucas Herrington opened the door for the home side.
Herrington tripped Bernardo, with Sawyer easily converting the penalty in the 66th minute.
The substitute striker had only come off the bench nine minutes earlier.
Macarthur's ascendancy continued when Roar midfielder Noah Maieroni grasped Sawyer's shirt for too long while moving into the box.
Sawyer again scored from the spot, celebrating his 73rd-minute goal by moonwalking in front of the home fans.
The substitute's heroics mean the Bulls, who started the round in 10th, can finish in the top-six at the end of round nine.
Macarthur are fifth (3-2-3), while third-placed Roar's (4-3-2) six-game undefeated streak is over.
Brisbane coach Michael Valkanis made no secret his frustration.
"We should have finished the game off, didn't get three points. I'm not happy, that's it," Valkanis said.
A concussion to centre-back Uskok put a damper on Macarthur's win.
Uskok had suffered the injury after the kick of Roar's Justin Vidic - who was offside - deflected off Bulls goalkeeper Filip Kurto's foot and on to his teammate's head.
Macarthur coach Mile Sterjovski was already without star midfielder Anthony Caceres, who picked up an illness following their ACL2 win over Beijing Guoan last Thursday.
"He's played the most games out of everyone in our club, so it will be difficult without him," Sterjovski said of Uskok.
"It's frustrating because it comes down to an offside, an obvious offside."
The home side were lucky to avoid conceding a first-half goal after struggling to find answers for Brisbane's relentless pressure and physicality.
Macarthur had just one shot at goal against the league's stingiest defence.
Brisbane had led the league with the fewest goals conceded, having given away just three goals before Friday's match.
Roar striker Jay O'Shea should have scored in the 17th minute when a lapse in the home side's defence left the ball up for grabs directly in front of goal.
But the Irishman sent his shot over the bar.
English striker Chris Long was the architect of the opening goal, winning possession in Roar's attacking half to kickstart a wonderful chain to Dench in the box.
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