Saints coach Ross Lyon masterminded a 61-point win over Fremantle eight weeks ago in Melbourne, and another upset was brewing at Optus Stadium on Sunday as the Saints surged to a 14-point lead early in the final quarter.
St Kilda dominated the clearances 39-16 across the opening three terms, but Fremantle won the key stat 15-7 in the final quarter to make their move.
Ruckman Sean Darcy marked a low ball and kicked truly to start the onslaught.
Luke Jackson, Josh Treacy and Isaiah Dudley followed it up with their own set shots as Fremantle shot out to a 10-point lead.
The margin was pegged back to just six points with 49 seconds remaining when Mitch Owens snapped truly, but Fremantle won the next centre clearance and Jackson pulled off a stunning mark in attack to ice the 11.15 (81) to 9.15 (69) win in front of 41,600 fans.
Fyfe, who only recently returned from a hamstring injury, would have been the perfect option to bring on in the final quarter, but the veteran felt discomfort in his calf while warming up at half-time.
"He tried to warm up at half time and he did some run-throughs and then he felt some awareness in his calf," Fremantle coach Justin Longmuir said.
"So, not sure whether we could have put him on if we had an injury, but since we didn't have an injury and didn't have any players really flagging, the safe option was to just leave him out of the game.
"It's a bit of a concern, of course. But we'll see how he pulls up tomorrow, get it scanned if we need to, and see where it takes us.
"But from what I understand, it's pretty minor and we didn't have to bring him on."
Fremantle's sixth straight victory improved their record to 10-5 ahead of a challenging away clash with Sydney.
St Kilda (5-10) fell further adrift of the top eight, in 15th spot.
Saints ruckman Rowan Marshall was superb, winning 10 clearances to go with 21 disposals and a goal.
But Dockers ruckman Darcy lifted massively in the final quarter to finish with 41 hitouts, 17 possessions, seven clearances and a goal.
Treacy kicked three goals for Fremantle, and Jackson chipped in with two in the last quarter.
Longmuir said defender Jordan Clark, who had 31 possessions and kicked a goal, was his team's best.
Much pre-match talk centred on whether Lyon would send tagger Marcus Windhager to Caleb Serong or Andrew Brayshaw.
The answer was neither, with Windhager released from his tagging duties, and teammates including Jack Macrae, Jack Steele and Hugo Garcia instead left to mind their more highly-rated opponents.
Brayshaw tallied 25 possessions and just two clearances, while Serong was restricted to 18 disposals but lifted in the final quarter to finish with nine clearances.
Former Docker Liam Henry was loudly booed each time he touched the ball. He answered back with a 'shoosh' motion to the crowd after thrusting St Kilda into the lead with a second-quarter goal.
Lyon, the most successful coach in Fremantle's history, was booed by home supporters when shown on the stadium's big screen in the final quarter, in his first match against the Dockers in Perth since being sacked by the club in 2019.
Dockers fans were left cheering at the final siren after watching their team escape with another close win.
Lyon chatted to former Dockers skipper Matthew Pavlich on the field before the match, and shared a special moment with Fyfe.
"I see Pav and there's special feelings. I see Fyfe, we have a hug," Lyon said of his return to Perth.
"As I used to say, whether it was Mark Harvey or me, or (Chris) Connolly, or Longmuir when he goes - because we all go, right? - you do your best, and then hopefully you're part of that club's history and it's respected, and you move on."
