The Wanderers recorded the 2-1 victory after going down a goal at Suncorp Stadium in the first half, and they now sit comfortably in fourth spot on 29 points to be just a point back from third-placed Melbourne Victory, but eight clear of fifth-placed Melbourne Heart.
The Roar could have gone within a point of entering the top-six with a victory and got off to a terrific start controlling much of the first half, and then putting a goal on the board through Mitch Nichols in the 22nd minute.
It was a lacklustre Wanderers outfit in the first half, but they came out rejuvenated in the second half to produce goals in the 65th and 69th minutes courtesy of Mark Bridge and Youssouf Hersi.
That was enough for Western Sydney to come from behind and win for the first time in what is their inaugural A-League campaign.
Western Sydney coach Tony Popovic knew that his team had to have a big lift at half-time, but he was confident of it happening and was delighted with their response.
"Of course it was possible at half-time. We didn’t play too well in the first half, but it was a good challenge for the players. We asked them to try something that we haven’t done yet and that's to come from behind, and you could see from the outset in the second half that we were on the front foot," Popovic said.
"I thought in the end we thoroughly deserved it. There have been a lot of firsts at this club obviously this season and today was another step forward for us. To come from behind shows the character and belief in this squad and it has been a great response since our loss against Central Coast.
"We have got six points from six available on two tough road trips, and we look forward to going home now."
Roar coach Mike Mulvey was left frustrated for a number of reasons. He did feel that Hersi's goal should not have been allowed due to Shinji Ono being in a passive offside position during the play, but he was more frustrated with the performance of his team in the second half.
"You're not going to have me using excuses about offsides or anything like that because the game goes until the referee blows his whistle," Mulvey said.
"I was very pleased at half-time and I thought we had played well in the first half aside from a lull for about 10 minutes, but we started with a better tempo from last week and our passing and movement was better.
"I thought we went into half-time with a deserved lead, but you can't give people like Ono and Mooy space in the middle. Hersi was given a bit too much space and we didn’t defend well enough. I'm not going to make any excuses. This is a team game and at times we switched off, and were playing with eight men."