It seemed destined to end scoreless until substitutes Mirjan Pavlovic and Alex Smith and goalkeeper Tony Warner conspired to hand Josh Mitchell too much space at the far post from where he headed home substitute Andrezinho's freekick.
The Phoenix probably had a case in challenging officials for what seemed a soft freekick but there was no excuse for leaving Mitchell unchallenged as he scored his first goal of the season.
Warner failed to cover his post, leaving a gap for Mitchell to spear the ball down and over the line.
The loss dents Phoenix hopes in their run at the playoffs.
Their first loss at home since losing 2-1 to now runaway leaders Central Coast Mariners in early November spoiled their chances of moving up the table but with other results going their way they held their spot in the top six but with the pack now yapping at their heels.
Controlled football was always going to be difficult but that alone could not be blamed for the early erratic passing from the Phoenix players in their attempt to make the most of the howling southerly at their backs.
Once they adjusted to the testing conditions, the visitors took the game to the Phoenix who were forced to call on all hands in a swarming defensive effort to blot the attacking threat posed by Shane Smeltz, Liam Miller and Steve McGarry.
Despite having more than 30 balls played into the respective penalty areas - and Perth led that statistic 23-9 at halftime - neither goalkeeper was really tested, with McGarry having the best chance with the last kick of the first half which he poked straight at Warner.
The home side had the better of the early opportunities in the second half with Daniel denied by Miller at the far post from a corner and later by the crossbar with a sweeping shot after good build-up play from Chris Greenacre and Leo Bertos.
Coach Ricki Herbert brought Pavlovic and Paul Ifill into the game with 30 minutes to play but they too failed to find the spark the team were looking for as they chased a match-winner.
Smeltz had a good chance in the 66th minute but he could only despair as his effort rattled the underside of the crossbar and stayed out.
A spate of three cards late in the match summed up the frustration felt by both camps but in the end the visitors had the final say as they picked up their first win since beating Gold Coast in early December.
The Phoenix now face away games with Gold Coast and Newcastle before playing the rampant Melbourne Heart at home on January 29.
