Perth started the stronger out of the two sides, having multiple early efforts at goal, but Bayswater opened the scoring in the 25th minute with a goal from David Heagney.
Perth SC’s Adrian Madaschi gave his side a crucial equaliser two minutes into the second half but Bayswater could not be stopped for long.
Bor Bor Sam curled the ball into the top corner to take back the lead and condemn Perth to their first loss of the season.
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Despite the positive result, Bayswater City coach Chris Coyne said he was not entirely happy with his team’s performance.
“I thought we were the side that had 70 per cent possession, but when you have that much possession, you need to take your chances,” he said.
“I’m not happy; I want more and I don’t want to concede sloppy goals.
“A free header from four yards out isn’t acceptable.”
Perth SC coach Ramon Falzon said he was frustrated with his team’s performance, with the loss knocking them off the top of the league ladder.