A controversial fourth-minute goal to United winger Matthew Grimaldi was all that separated the teams in Sunday's match at Ironbark Fields.
United (44 points) moved to third spot, just one point adrift of second-placed Melbourne City with a game against premiers plate winners Auckland FC to round out their regular-season campaign.
The situation is perilous for Sydney, who need a win or a draw against Melbourne City at AAMI Park next Saturday to secure sixth place.
If Sydney fail in their task, Adelaide will secure a finals berth.
That match also looms as critical for Western United, given a Melbourne City loss or draw would give them a chance to steal second spot and an AFC Champions League Elite berth.
Western United coach John Aloisi was pleased with how his team bounced back from defeats to Western Sydney and Brisbane Roar.
"It was a tough game. We knew it wouldn't be easy. Sydney needed at least a point to secure finals," Aloisi said.
"I thought defensively we were good, not only the back four, but everyone.
"We scored a really good goal. I'm really pleased with the players because it's been a tough week.
"We just wanted to make sure we got back to winning ways.
"We want to try to see if we can finish as high as possible. We know we're only one point away from City now.
"Hopefully Auckland are still celebrating (their premiers plate trophy)."
Sydney coach Ufuk Talay was left fuming when the referee missed what appeared an obvious foul in the lead up to Western United's opening goal in the fourth minute.
Sky Blues defender Joel King was put on his backside after being bumped in the air by Michael Ruhs just moments after heading a ball.
With King unable to get up in time, Western United swung the ball forward for Riku Danzaki to cross to Matthew Grimaldi at the far post for an easy tap-in.
Ruhs almost doubled the lead in the 34th minute, only for his shot from the tightest of angles to hit the post.
The woodwork also came to Western United's defence, with Adrian Segecic's thunderbolt from the edge of the box rifling into the upright.
"They had a good counter, which I thought was a foul on Joel King, but the referee deemed it wasn't," Talay said.
"I thought it was a little bit late. I think Joel wins the header and Ruhs comes in a little bit late, and the connection is there.
"I'm disappointed we lost the game. We need to pick up at least one point against City to make the finals."
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