Swedish attacking midfielder Ola Toivonen set up the first goal for the Victory, scored by Kosta Barbarouses, and added one of his own in the 81st minute.
The Phoenix scored three first-half goals in 17 minutes, with striker Roy Krishna netting twice. Defender Michael Zullo pulled a goal back in the 89th minute, but Sydney sustained successive home losses for the first time since April 2016.
Western Sydney beat last-place Central Coast 2-0, the Mariners' fifth loss in seven matches.
On Sunday, Newcastle defeated the Brisbane Roar 2-0 in the final match of the round.
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