Roar made a dream start, scoring the decisive goal in just the second minute through young forward Brandon Borrello.
Borrello was fed in by Thomas Broich and unleashed a fierce drive from a narrow angle, the shot whizzing past Japanese international goalkeeper Shusaku Nishikawa at his near post.
It was all Roar needed to seal its first ever victory in Asia and pick up a vital three points in Group G after the disastrous 1-0 loss last week to Beijing Guoan.
The host spent most of the second half a player short after Daisuke Nasu was shown a straight red card for bringing Andrija Kaluderovic to the ground with a cynical rugby-style tackle, just as the Serbian striker appeared set to streak through on goal.
But unlike how it coughed up the ascendancy to a 10-man Beijing, this time Brisbane was able to seize the advantage.
It wasn't all smooth sailing - Roar's inability to put Urawa to the sword with a second goal made for some nervy moments but, led by Luke DeVere, the defence was ultimately able to keep the Reds at bay.
Coach Frans Thijssen made four changes to the team that drew 2-2 in Perth at the weekend, with the most notable omission being goalkeeper Michael Theo, who suffered a groin strain against Glory and was named on the bench against Urawa.
Theo's understudy Jamie Young started in the goalmouth while Henrique overcome a knee injury to take his place in the team - but there was no room for ex-Socceroo Adam Sarota, who was left on the bench for the second straight game.
Henrique spurned a great chance to make it 2-0 in the 35th minute, again on the back of a Broich through ball, but Shusaku was able to make the stop with his foot.
Young stood tall shortly after the interval, protecting Brisbane's lead with an excellent save of his own to deny Urawa's Koroki Shinzo, who was clear on goal and hovering around the penalty spot.
Minutes later, the home side was reduced to 10 men when Nasu needlessly felled Kaluderovic, turning the contest Brisbane's way.
Substitute Tadanari Lee nearly equalised for Urawa at the death but his diving header flew just over the crossbar.
Borrello said there was a concerted effort from Roar to throw everything at the J.League powerhouse in attack from the outset.
"We wanted to start aggressive in the first couple of minutes and get a few shots away. A bit of luck to us that the first shot went in," the striker said.
"But the fact we were aggressive for the whole game, everyone worked as a team just like we planned out - it was great to get the win.
"To beat a top-quality side like that, it's a great achievement.
"We're going to take it in our stride and go on next week, bring it to the A-League and hopefully get three points."
Borrello said it was that very mindset that led to him chancing his arm with the third-minute goal, a rocket of a shot from a tight angle that beat Japanese international goalkeeper Shusaku Nishikawa at his near post.
"In training I work with Rado (Vidosic), receiving it outside the six-yard box," he said.
"Depending on where the keeper is, you'll probably try to hit it across the keeper.
"But I thought, you know what - we've gone with the intent to test the keeper as early as we could, so I figured why not have a shot?"
Thijssen was beaming with pride after the match, praising his entire squad for executing Brisbane's tactics to perfection.
"They did exactly what we planned to - attack early and then soak up the pressure we knew would always come from Urawa," he said.
"We deserved this win."
