Roar needed a victory to have any chance of reaching the knockout stage but came up well short against the Group G also-ran in front of a meagre crowd of 5941 at Robina.
The defeat marked the final match at the helm for interim coach Frans Thijssen with his likely replacement, Spaniard Ramon Tribulietx, thought to be in Brisbane for talks over taking the reins next season.
Beijing Guoan and Suwon Samsung Bluewings fought out a 1-1 draw in the other Group G game which was played at the same time, consigning the Roar to a third-placed finish.
It is the third time Brisbane has failed to make the knockout stages of the tournament in as many attempts.
After a bright start, Brisbane, which had bombed out of the A-League finals against Adelaide last Friday, was quickly rocked back on its heels as Urawa broke with pace and purpose.
Keeper Jamie Young denied Urawa captain Shinzoh Kohrogi with a smart save in the 20th minute and he was called into action again to thwart the same man as he broke through one-on-one three minutes later.
But he was powerless to prevent Kohrogi from making it third time lucky in the 24th minute as he latched onto a clever through ball from Keita Suzuki to steer a low left foot shot past the despairing dive of the Roar keeper.
Brisbane struggled to create clear cut chances against the group's bottom team with its thrusts forward were more ponderous than penetrating.
Roar's plight become hopeless in the 57th minute when substitute Yuki Moto - who had only been on the field a matter of seconds - produced a sublime left-footed finish from a tight angle after being released by Toshiyuki Takagi.
Brisbane offered little in reply with Devante Clut's skied effort summing up its efforts until it finally made a breakthrough in the 70th minute when Clut fed Andrija Kaluderovic and he produced a neat angled finish to lift his side's spirits.
Brisbane came on strong late on but it was too little too late.
Curiously, Thijssen did not use any of his substitutes, a decision he said was made because the Roar had no experienced defensive back-ups.
"We had to solve a lot of problems because we missed our whole defence," Thijssen said, referring to the injury-enforced absence of Shane Stefanutto, Jade North and Luke DeVere.
"They had to play one-against-one really ... Urawa played with five strikers most of the time.
"That's why there was for me no reason to change anybody else, we had no defenders on the bench except for young (Lachlan Jackson)."
Urawa coach Mihailo Petrovic refused to criticise Thijssen's substitute abstinence, but praised the Roar for its style of play.
"Both teams played wonderful football, with great passing," he said.
"But we could have had two or three more goals in the first half. Overall, we thought we deserved the win."
