The Lions conceded the opening four goals, seized control then withstood a final-quarter fightback at the SCG, further demoralising the same opposition they crushed by 10 goals in the 2024 grand final.
Brandon Starcevich suffered a concussion in the fourth quarter, Charlie Cameron was a late scratching because of a calf strain, and livewire Kai Lohmann (ankle) was substituted early on.
Dual Brownlow medallist Lachie Neale failed to touch the ball in either the second or third quarters as tagger James Jordon curbed his influence.
Isaac Heeney's late goal put Saturday's scrappy match in the balance with 63 seconds remaining, but Brisbane stood up in a frantic finish to prevail 12.14 (86) to 12.10 (82).
Fagan praised his side's will to win, especially given Cyclone Alfred prompted the postponement of their season-opener and an earlier-than-planned departure to Sydney.
"One of our great wins," he said, beaming after a memorable debut for Levi Ashcroft.
"We had an interrupted preparation for this game, with the cyclone threat up in Brisbane.
"That's an awesome win. Sydney are hard to beat at this ground, they're tough .. they threw everything at us. They took Lachie Neale out of the game.
"We lost Linc McCarthy during the week too with his knee. So there were a lot of forces that felt like they're working against us, but we found a way. I'm bloody proud."
Dean Cox struck an optimistic note as his side slipped to 0-2 ahead of a trip west to face Fremantle.
"Everyone's disappointed … I'd like to be in a better position but this group is really confident it'll turn very quickly," Cox said.
Perennially underrated forward Zac Bailey was arguably best on ground, kicking four goals, while Dayne Zorko and Logan Morris also helped their side kick a winning score with some highlight-reel fodder.
Starcevich, who also suffered a concussion in a pre-season game, was helped off the field after an accidental clash of heads with Sydney's Justin McInerney.
The defender will miss at least a round-two clash with West Coast, while Fagan noted star forward Cameron's omission was a "very cautious call".
Multiple turnovers, errors, fumbles, dropped marks and questionable decision-making meant the game often felt like the antithesis of a grand final.
That is to be expected from any fixture in mid-March, let alone one played in the hottest part of an unseasonably warm day in which the temperature in some parts of Sydney hit 38C.
"We looked really scratchy in the first quarter, made a lot of mistakes," Fagan said.
"I can't tell you how much of an effect the interruptions over the last two weeks have had, but it probably would have been some sort of influence on performance."
Chad Warner and Nick Blakey were among the Swans stars guilty of uncharacteristic mistakes.
A poor turnover from Matt Roberts, whose kick in defence picked out Lions gun Dunkley and gifted the visitors a decisive goal in the arm-wrestle of a final term, was particularly costly.
