The Magpies were razor sharp early and had chances to build a lead of note early in the second quarter on Thursday.
But they lost their way, the Lions kicking 10 straight goals to end Collingwood's unbeaten start to the season in a 18.8 (116) to 11.17 (83) victory.
McRae was able to routinely mastermind against-the-odds wins in his maiden season in charge last season.
But the coach admitted the medium-term absence of injured ruckmen Mason Cox and Darcy Cameron will prove tricky to overcome.
"There's no quick fix, there's no magic dust to it, we've got what we've got and we have to work through it," he said of their bandaid solution, with Daniel McStay and Billy Frampton sharing the duties.
Collingwood scored more from stoppages then Brisbane, but gave away precious ground that swayed momentum while the Lions defence was able to break down the usually-slick Magpie ball movement.
"We gave them gifts, there's no excuses, that's in our control," McRae said.
Cam Rayner kept Brisbane in it, then blasted them clear with four goals and 10 score involvements after being shifted from defence into his customary role up front.
He marked strongly, crashed tackles and distributed with poise to the delight the sell-out 33,565 crowd.
And he was often to thank when Charlie Cameron (six goals) burst on to the scene, the small forward's brilliant step and sideline dash all but sealing the deal early in the fourth quarter.
It was a crucial win as the Lions (2-2) responded from a flat loss to the Western Bulldogs last week that had landed tall forwards Eric Hipwood and Joe Daniher in the crosshairs.
Jack Crisp kicked a fourth-quarter goal but was otherwise quiet, the Magpies star playing a day after a video was leaked that will be the subject of an AFL investigation.
Nick Daicos (38 disposals, two goals) was brilliant but, incredibly, had only one disposal in the second quarter when the Lions, trailing by 13 at the first break, bit back.
Hipwood and Daniher (both two goals), who had a team-high 13 disposals at halftime and 20 for the game in a week his work-rate had been questioned, were both physical and took their chances.
"I was glad that we played well tonight, but I didn't think the picture that was painted last week, I didn't think it was as bad as that," Fagan said.
"I think the reason we won the game was that we were brave enough to come forward and get some intercepts on the handball chains, and we were able to score off those.
"You've got to do that well against them; if you retreat, they'll just run straight through you."
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