In a game of high drama and controversy on Sunday night at HBF Park, Popovic Jr rose high to head home and put his side up 2-1 in the 76th minute, sparking wild celebrations among the 5,893-strong crowd.
Just minutes later, Popovic was at the centre of an all-in melee when he shoved Tomislav Uskok to the ground after a crude tackle from the Macarthur defender.
The win was sealed in the 95th minute when former Melbourne City attacker Arion Sulemani charged forward on the counterattack before slotting his shot in off the post.
Although Glory's finals hopes were killed off before the match when Melbourne City beat Wellington 2-0, the victory at least lifted Perth six points clear of last-placed Western Sydney in the race to avoid the wooden spoon.
Macarthur's finals hopes are now hanging by a thread, with Mile Sterjovski's men four points adrift of sixth-placed Melbourne City with only two games remaining.
VAR came to Macarthur's rescue twice in the first half.
Their veteran Luke Brattan was given his marching orders in the fourth minute for what at first appeared to be a studs-up challenge on Nicholas Pennington.
Replays showed Brattan had lowered his foot by the time he clattered into Pennington, with VAR replacing the red card with a yellow.
Then in first-half stoppage time, Glory were awarded a penalty for a Liam Rose handball.
Replays showed the ball deflected off Rose's knee before clattering into his moving fist, with the crowd booing loudly after VAR stepped in to cancel the penalty.
Glory opened the scoring in the 48th minute, and it all started with a Pennington back heel.
Sam Sutton collected that deft pass and fired in a cross, the ball clipped Sebastian Despotovski as he attempted to jump over it, and Pennington ran to the right spot at the right time to fire home.
The entire team ran to the club's massage therapist Sharon Bamber, who lost her father during the week, to celebrate with a group hug.
"That's the nature of this group - they are all very kind and caring people," Glory coach Adam Griffiths said.
"That meant a lot to her, and it meant a lot to me as well."
Luke Vickery equalised in the 68th minute when he was able to dribble forward without a Glory defender closing him down before firing in a shot from outside the box.
Stefan Colakovski's pin-point cross set up 22-year-old Popovic for his maiden A-League goal in his 20th appearance, with his dad Tony celebrating in the stands.
And Sulemani also scored his first goal when he netted in stoppage time, ensuring his club's eight-match winless run came to an end.
"He really deserved that moment and that goal in front of the shed, and I think he'll cherish that," Griffiths said of Popovic.
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