Phoenix opened the scoring just before half-time through David Ball, who latched on to Tomer Hemed's backheeled pass before finishing into the bottom-left corner past Adam Federici.
A lightning start to the second period had Phoenix 2-0 up within a minute of the restart, Hemed converting a simple tap-in after the ball fortuitously fell for him in the box.
Things went from bad to worse for the Bulls just before the hour as Loic Puyo had a yellow card upgraded to a red by VAR (video assistant referee) after catching Ulises Davila on the knee – the Mexican and his Phoenix team-mates showed sympathy with him, however, with replays showing the Frenchman had attempted to pull out from the collision.
Hemed had the chance to make it 3-0 in the 85th minute but saw his penalty saved after Lachlam Rose brought Louis Fenton down in the box.
But the visitors did get a third goal in stoppage-time, Ben Waine collecting Ball's pass and slotting in just three minutes after replacing the lively Reno Piscopo.
Phoenix's performance was one of a team that should be in the finals, but it end the season a point behind adrift of the top six, while Macarthur's first A-League campaign continues.
The Bulls go into the finals as the lowest-ranked team, meaning it will not be able count on home advantage – not that it did it much good here – in its elimination-final.