Playing without stars Aine Tighe and Gabby O'Sullivan, the Dockers fought a relentless Saints unit to secure a 3.7 (25) to 2.2 (14) win at RSEA Park on Friday.
Star goalkicker Tighe, arguably the Dockers' best player, was ruled out of the season after rupturing the anterior cruciate ligament in her right knee in their round-four victory over Melbourne.
O'Sullivan, who kicked three goals against Melbourne in Tighe's absence, was made to serve a one-match ban for striking the Demons' Sinead Goldrick.
Midfielder Dana East suffered a concussion in Friday's third term, creating another injury headache for the Dockers.
St Kilda have now suffered two consecutive losses after Hawthorn handed them a 57-point thrashing in round four.
"It was a grind. There's no other way to put it," Saints coach Nick Dal Santo said.
"It was probably a hard watch. For those that were here or watching on TV, it was hard in the coaches' box.
"Just a lack of flow from both teams. That was probably the most disappointing thing that we couldn't break it open."
Mim Strom stood up to lead Fremantle with 13 contested possessions, five clearances and 18 disposals, while teenager Tunisha Kikoak led in attack with two goals.
St Kilda's Darcy Guttridge takes a mark against the Dockers. (Rob Prezioso/AAP PHOTOS)
Fremantle's win marked former captain Hayley Miller's 75th game and defender Emma O'Driscoll's 50th match.
Lisa Webb's charges conceded the opening goal and were scoreless at quarter time after Saints star Nat Exon audaciously sold some candy to Ariana Hetherington just in front of goal for a seven-point lead.
Kikoak then took a leaf out of Exon's book to bamboozle Grace Kelly for the Dockers' first major to open the second quarter before slotting another to send her side in front while Exon left the ground with a shoulder complaint.
But Fremantle's lead was brief, with sharpshooter Jesse Wardlaw restoring a one-point lead courtesy of a free-kick paid against Hetherington for holding.
Exon returned to the fray in the third quarter as Fremantle came out firing.
The Dockers were able to lock the ball in their forward half with six of the first seven inside-50s of the third term, but found little scoreboard reward for effort.
Miller was able to level scores when her running shot at goal hit the post before more skewed shots earned Fremantle the lead.
No goal was scored by either side in the third term and the Dockers arrived at the last break ahead by four points.
With 30 seconds on the clock in the final quarter, Miller launched to an empty forward-50 before Gabby Biedenweg-Webster chased down the Sherrin for the match-winner.
"I wish we could get it done a bit earlier," Fremantle coach Lisa Webb joked.
"At times, it was certainly challenging navigating a few things that happened during the game but once again, really happy to grind it out."
Jaimee Lambert (22 disposals, five clearances, 13 contested possessions) was the light for St Kilda, while defender Serene Watson fought valiantly with 23 disposals.
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