Lowe rued his side's wastefulness early in the game and some critical defensive errors which he said cost them the match.
It took the ladder-leaders until the 57th minute to break down a resilient Glory defence, and when the opening goal came it was via a set piece, with Ivan Franjic getting his head to a Thomas Broich cross.
After the home side had taken the lead there appeared no way back for Perth, as former Perth midfielder Liam Miller and Broich added their names to the score sheet before Shane Smeltz's injury-time goal.
Lowe's side had burst out of the blocks to create a series of early chances, but failed to capitalise before Brisbane took charge of possession.
"You can't do two things against this side," Lowe said.
"You can't not take your chances, and we had one or two that were half decent, really early on in the game that may have changed the dynamic.
"And then you can't give them the first two goals, because there's no coming back from that."
The England-born coach said that once Brisbane took the lead, their seasoned players were always going to push home the advantage.
"At the end of the day we've got a number of inexperienced guys and they've got a number of experienced guys in their top third and their experienced guys produced where our inexperienced guys did ever so well for so long, but the odd lapse here and there, it just hurts you, especially when they've got the quality that they've got."
Perth's backline contained veteran Frenchman William Gallas plus three youngsters, and it was a mistake by centre-back Brandon O'Neill, who had moments earlier been cramping up, which gifted Brisbane their second goal.
Lowe expressed little sympathy for the 19-year-old, but said his blunder would prove a learning experience.
"No, I don't feel sorry for him," he said.
"You know why? Because it will make him, he'll remember it.
"It won't be a nice experience but he'll remember it, it will be burnt in his memory, and he'll have a little bit of pain.
"And you know what? He'll be better for it, the kid."
