The Roar were out to repeat their round-four 3-0 drubbing of the Jets in a bid to snap a dismal form slump, but it was all Newcastle at McDonald Jones Stadium on Saturday.
So dire were the visitors that Brisbane coach Michael Valkanis slammed his side's performance as "unacceptable".
Newcastle lived up to the "Box Office Jets'' billing, with in-form striker Lachie Rose converting a penalty kick in the 18th minute to open their account in front of 12,162 fans, before Clayton Taylor's 52nd-minute goal.
Roar defender Dimitri Valkanis hit back in the 62nd minute, but Bayliss snuffed out any chance of a Brisbane comeback by restoring the two-goal lead less than a minute later.
Brisbane were reduced to 10 men in the 90th minute when English striker Chris Long was shown his second yellow card for fouling Taylor, before Bayliss completed his first career double two minutes into added time.
Long had fouled Eli Adams in the 39th minute for his first booking.Â
Newcastle's remarkable revival under first-year coach Mark Milligan continues. The Jets have a chance of finishing outright first if Auckland fail to beat Perth Glory later on Saturday.
The Jets are now on a club record five-game winning streak and boast 27 points, with Auckland on 25.
Still, Milligan has so far kept the lid on his side's rise.
Asked about the "Box Office" mantle, Milligan said: "No, no, no. It was a better performance, it was a very professional performance.
"Our mentality has to be, you know, 'It's done'. We have to work again tomorrow."
Brisbane have suffered a reversal of fortunes since last meeting the Jets in round four, slipping from third to seventh (6-3-7) in the new year.
A suspected hamstring injury to captain Jay O'Shea in the 35th minute only added to Brisbane's woes.
"We were a shadow of what we've been in the past," Valkanis said.
"You can lose games, but not like this. To me, this is unacceptable."
Taylor set the tone early in front of the club's biggest home crowd since the 2018 grand final loss to Melbourne Victory, bamboozling the Roar defence with a daring run down the left wing in the seventh minute, before firing off a cross to Rose.
Rose couldn't get to Taylor's pass but made up for the missed opportunity by scoring the opener, after Newcastle goalkeeper Dean Bouzanis gave away a penalty for fouling Taylor in the 16th minute.
Bouzanis had taken Taylor to ground in an attempt to intercept a lofted ball from Newcastle midfielder Will Dobson.
Rose found the back of the net in the 61st minute after combining with Taylor again, but the goal was chalked off for offside.
Brisbane fired off just eight shots to Newcastle's 18 and had less than half the amount of possession in a lacklustre performance.
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