Mills was on crutches by halftime at the SCG on Saturday after he went down with a suspected serious knee injury late in the first quarter.
The Swans made a hot start and led 40-8 when Mills' right knee gave way as he attempted to corral Lions ball-carrier Will Ashcroft near the boundary line.
Fans held their breath as Mills was helped off the ground by two Swans trainers, accompanied by a large round of sympathetic applause as the 29-year-old made his way down the race.
Mills reappeared on the bench and gave a thumbs-up to fans when he was shown on the big screen, riding the bumps with his teammates as they completed a stunning 21.15 (141) to 13.10 (88) triumph.
It set up a home preliminary final against either Fremantle or Geelong in a fortnight.
The upset victory followed a tumultuous few weeks in the fallout from the Pullman Hotel scandal, which past players have admitted shattered the club's famed "Bloods culture''.
"It's unbelievable. I'm so proud," Mills told Seven after Saturday's win.
"We wanted to build some respect back, and the way we turned up tonight, the way we fought - it was Bloods-like and I'm so proud of the group."
Mills faces scans on his injured knee, which appear set to rule him out of action for the rest of the finals series as Sydney chase an unlikely premiership without several of their biggest stars.
"We'll figure it out later," Mills said of the injury.
"It is what it is. I'm just so proud to be a part of this group.
"That was a special win. Sitting on the bench and being a part of it was incredible.
"I hope everyone here that felt it today feels the same because I'm really proud to be a Swan."
Mills also faces the prospect of missing a large portion of next season.
It comes amid speculation over the playing futures of the five Swans teammates - including stars Isaac Heeney, Chad Warner and Nick Blakey - who were suspended for breaching club behavioural standards last month.
Mills had earned plenty of kudos for his leadership after the Swans were plunged into crisis by the Pullman Hotel scandal, which led to the club-imposed player bans.
The latest setback could be another significant injury for Mills, who missed most of the 2024 season after hurting a shoulder in a "Mad Monday'' wrestling contest with a teammate.
Mills returned to action late in 2024 and played in Sydney's first final, but injured a hamstring and was sidelined when the Swans lost to Brisbane in the season decider.
Swans forward Logan McDonald said he was "shattered" to see Mills go down with the knee injury.
"He's the heartbeat of this club, with what he's had to do over the last couple weeks to represent the club and be the face of the club," McDonald said.
"I have absolute admiration for everything he does, and the way he plays footy. I'm absolutely gutted for him."
Sydney firebrand Tom Papley backed the Swans to respond positively to the Mills injury after showing great spirit against Brisbane.
"We won today without Millsy, so that adds to the win as well," Papley said.
"It is what it is. We'll re-group, we've got a couple of weeks to work out who comes in for Millsy. But yeah, we'll get to work."
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