It was a valiant effort from the Roar, who were recharged after a nine-day break and keen to atone for their horrendous 6-0 thumping against Ulsan Hyundai in their most recent Asian outing.
But while they had their moments in Tuesday night's clash at Kashima Stadium, they lacked the clinical touch of the reigning J-League and Emperor's Cup winners, who were simply ruthless in front of goal and much more penetrative with their play.
It leaves John Aloisi's side winless and on the bottom of Group E after suffering the fifth defeat by an Australian side in this year's tournament.
They are also yet to find the back of the net in three matches.
Rising Japanese star Yuma Suzuki opened the scoring in the 43rd minute with a first-time stab at an enticing cross from right-back Yukitoshi Ito.
Jamie Young - who is being used by Aloisi as the Roar's dedicated Champions League goalkeeper - didn't react in time at his near post and was also at fault for their second goal from a 76th minute corner.
The gloveman failed to secure a header from Naomichi Ueda, who pounced on confusion in the box by following up his effort and bundling it over the line with his shins as Young scrapped to recover.
Three minutes later, Yasushi Endo beat his marker Corey Brown and curled in a left-footed shot to put the final nail in Brisbane's coffin.
Young's blunders undid his good early work in the goalmouth as he kept the Roar in the match with a number of athletic diving interventions.
Missing first-choice players Tommy Oar (hamstring), Thomas Kristensen (thigh) and Luke DeVere (calf) as well as the rested Michael Theo, the best chance for the visitors came midway through the first half, when Brandon Borrello trickled a ball into the box towards Jamie Maclaren.
The striker unselfishly left it for Brett Holman, but his dummy seemingly surprised the former Socceroo, who reacted late and scuffed a meek shot from point-blank range that was tipped wide for a corner when he should have scored.