Lions captain Harris Andrews ruled with an iron fist while Charlie Cameron and Cam Rayner shone up front in Thursday's 19.12 (126) to 12.11 (83) well-rounded triumph.
Chad Warner (four goals, 28 disposals, eight clearances) offered up a goal-of-the-year contender with his long-range solo effort while Errol Gulden (18 touches, six tackles in 77 per cent game time) was quiet in his return from a long-term shoulder injury.
Both sides were coming off a bye and Fagan clearly made the most of the extra time, orchestrating a complete shut down of the flowing offence that had taken the second-placed Swans to 12-2.
Brisbane (9-6), who have played in the past three grand finals, have now won three successive games after losing as many in a row and having their status as contenders questioned.
The Giants, Fremantle and Geelong had peeled back the Lions' defences this season but the hosts were emphatic on Thursday, rushing the Swans to halt their usually potent handball game and create offence of their own.
"It's a bit nerve-wracking, but that's how you've got to play against them," he said.
"Seems to me we play better defensively when we go hard on attack and back ourselves in."
Cameron (two goals) and Rayner (three) were both lively in front of goal, while Logan Morris (three) benefited from their impressive forward pressure and Zac Bailey (two goals, 20 touches) was a handful.
Warner kept the Swans in it and his first two goals come from Lions turnovers and his third was a brilliant solo effort.
Reading Lachie Neale's (27 disposals, seven clearances) chip kick, he smothered and took off, bouncing three times and stepping past Ty Gallop before slotting the goal.
Brisbane weren't deterred though and a 50-metre penalty gifted Darcy Fort a goal before Rayner's third put the game to bed before three-quarter time.
The margin should have been greater at the final break, but Logan Morris was curiously deemed to have played on when he snapped his set shot after the siren and had his major taken off him.
Fagan felt his man was hard done by and said he'd seek clarity with the AFL and prompt Morris to kick a drop punt in that scenario instead.
"He did it thinking he was doing the right thing, but if he wasn't we need to learn from it and that's okay," Fagan said.
The margin meant it mattered little as Kai Lohmann cashed in late with two final-quarter goals and the Lions tuned up for a trip to Geelong next Thursday.
The Lions had six players kick at least two goals while Will and Levi Ashcroft both had eight clearances and Sydney's Isaac Heeney added seven clearances within his 30 touches.
Sydney's loss followed three and two-point wins before their bye in the last round.
"That's what you always get, opportunities to learn and level out where you're at and we've always held Brisbane in the highest regard and they showed why," coach Dean Cox said of failing the Lions' litmus test.
