Alana Murphy and former Sky Blues striker Rachel Lowe scored first-half goals, before Emily Gielnik lashed in a superb third just after the hour mark.
Alex Chidiac added the exclamation point, racing clear in injury time and finishing coolly.
The result is season-defining, with Sydney FC now needing a favour from Perth Glory against Melbourne City to win the premiership.
Victory also jump from seventh to fourth, bumping Western Sydney out of the top six.Â
Given the consequences, Whyman will regret a petulant ankle-tap of Victory forward Chidiac, a retaliatory kick after the fellow Matildas player had bumped her with the ball.
The brain-snap drew a yellow card and brought Lowe to the spot, and she scored to send Victory 2-0 up.
Earlier in the first half, Murphy lashed home from close range after Sydney FC failed to deal with Kayla Morrison's powerful header from Beattie Goad's corner.
On 64 minutes, Gielnik netted her seventh goal in seven games when her first-time flick from Jamila Rankin's cut-back beat Whyman at the near post.
The surprise result means Sydney FC, the three-time reigning premiers, face an agonising wait to learn if they will defend the Premiers Plate.
They have 39 points, with second-placed City on 38 and able to leapfrog them with a win in their Sunday night kick-off away to Perth Glory.
Victory, meanwhile, locked up fourth with the most consequential Big Blue since the 2022 grand final, the last time Victory had beaten their arch-rivals.
Both the title and the finals make-up hung on the result, with Sydney able to lock up the premiership with a win, and Victory needing to avoid defeat to make the top six.
There is also heartbreak for Western Sydney, who miss out on just their second finals outing in 12 seasons.
Victory's win also means the first week of the finals - after a week off for international matches - will take place in Melbourne.
Third-placed Western will host Newcastle Jets, while Victory's prize for jumping to fourth is a home final against Central Coast.
Sydney FC - who may have thrown away the title in the past week, given their 1-0 loss to second-bottom Canberra United on Wednesday - are at least assured of a top-two finish.
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