The in-form Sky Blues nearly blew it as Roar launched a late fightback at rain-lashed at Allianz Stadium but survived a bruising finale to jump from fifth to second, just a point adrift of leader Wellington Phoenix.
A thrilling victory also saw Graham Arnold's men equal a club record run nine games unbeaten, as Janko also shattered Alessandro Del Piero's previous club record of 14 goals in a season by two.
Brisbane got off to a dream start with Brazilian livewire Henrique bursting onto Jean-Carlos Solorzano's flicked through ball in the fifth minute to skip clear and send an angled finish past goalkeeper Vedran Janjetovic.
TV replays showed the diminutive striker was marginally offside, but got the benefit of the doubt from the match officials to give Frans Thijssen's men the early advantage.
But it didn't last long, with former Roar defender Matt Jurman blasting the Sky Blues level two minutes later as he latched onto a Janko back-heel off a long ball from Nikola Petkovic to bury a stunning shot past keeper Jamie Young.
His counterpart Janjetovic did well to keep out a Jerome Polenz piledriver in the 21st minute and two minutes later Solorzano fired over from point-blank range with the goal gaping as he got on the end of Corey Brown's cross.
Janko was denied by Young in the 35th minute, but he made no mistake two minutes later to stroke home his 14th goal of the season from the penalty spot after Adam Sarota had pulled back Alex Brosque in the box.
The strike set a new A-League record for the Golden Boot leading Austrian as he scored for the seventh game in succession to better Besart Berisha's previous tally of six and move closer to securing a new contract with the Sky Blues.
Young denied Sydney a third in the 48th minute as he dived low to keep out Brosque's goal-bound effort after the skipper had exchanged passes with Chris Naumoff.
But he could do nothing to prevent Janko burying his second with a tap-in from Naumoff's pin-point cross in the 52nd minute to give the home side a two-goal buffer.
And he completed his hat-trick in the 75th minute with another spot-kick, blasting the ball past Young after being fouled by Brown.
Brisbane was handed a lifeline in the 79th minute when Petkovic bowled over James Donachie and substitute Andrija Kaluderovic planted the spot-kick past Janjetovic.
And Sydney's nerves were jangling in the 84th minute when substitute Steve Lustica pulled another back with a neat finish after being teed up by Brandon Borello.
But it seemed as if Sydney had killed off the game when substitute Shane Smeltz cut the ball back for Brosque to steer his shot past Young in the 89th minute, only for the game to take another twist 60 seconds later when Borello caused more havoc down the right and the ball fell to Dimi Petratos, who thrashed his shot home.
Brisbane remains in seventh spot, two points off a play-off spot, but with two games in hand on sixth-placed Melbourne City.
A relieved Arnold said: "I must have a strong heart, it's been tested of late but we're playing really good football.
"Defensively we talked about tightening things up, but look it comes down to concentration. You're up 4-1, go for 5-1. That's what a top team does and that's stuff that we have to work one and stuff we need to move forward on.
“Our attacking play and the way we're moving the ball is outstanding but I think tonight was as good a game in possession as probably any the supporters have seen Sydney FC play in the last 10 years."
Arnold said of hitman Janko: "He has bought into everything that we're doing here and he's in great shape.
"We keep on improving, we keep on working and Marc values the team importance more than the individual performance.
“There was never any time that he thought about the records today. I got him to make a speech to the players before the game because they were poor in the warm up and Marc's speech to the players was all about supporting your team mates and we have to work hard together.”
