It was Brisbane's first pre-season flag, to go with their three grand final triumphs in 2001-03.
Brown kicked five goals, including two in the third quarter as Brisbane made their decisive break, at Etihad Stadium on Friday night.
Small forward Josh Green kicked three majors for the winners.
But the Blues did not have a multiple goal-kicker.
With Carlton almost certain to enter the season proper without their best key forward Jarrad Waite (calf), they lack a stand-out target, with the likes of Shaun Hampson, Levi Casboult and Sam Rowe failing to convince.
The Lions will enter the season unbeaten, while the Blues, who started so strongly under new coach Mick Malthouse, ended their pre-season with back-to-back defeats.
The Lions dominated early.
After the Blues kicked the night's first goal, from a Mitch Robinson free kick, Brisbane kicked the next five to build a 27-point lead late in the first quarter, with Daniel Rich and ex-Melbourne recruit Brent Moloney well on top in the midfield.
Rich won the Michael Tuck Medal for best afield.
Carlton narrowed the gap to 12 points at the first break, boosted by a Bryce Gibbs nine-pointer.
Gibbs was again prominent as Carlton kicked three goals in the first six minutes of the second term, capped by a Zach Tuohy nine-pointer, on their way to building a 13-point halftime lead.
But it was all Brisbane after that.
The visitors kicked five goals to one in the third term, including two Brown majors, to surge clear.
Rich was again crucial in Brisbane's run.
Exciting youngster Dayne Zorko, Pearce Hanley and Patrick Karnezis were all influential, while Daniel Merrett was strong in defence.
Carlton never looked like recovering, as Brisbane pushed further clear in the last quarter.
Ruckman Matthew Kreuzer was the Blues' best, with Kade Simpson, Kane Lucas and Gibbs all handy, but Chris Judd was quiet in his return from injury.
Lions coach Michael Voss said the players could enjoy their win on Friday night, but by Saturday needed to be concentrating on their round one clash with the Western Bulldogs.
He said their pre-season would give the team great confidence, particularly about their ability to finish games strongly.
"I reckon every single week we've been able to finish out the games really strong so that's a really good asset to have going into the season," Voss said.
Malthouse said the Blues were terrible.
He said they were beaten soundly at the contests, didn't run hard enough and surrendered the game too easily.
He said it might take two to three months to iron some issues out.
"I'm a realist. Things don't change just like that in football clubs," he said.
"You've just got to make sure you stay sound and each week you keep chipping away and getting better."