But Cox's premiership dream remains alive, with the 28-year-old to have one final chance to push his case for a recall this year when he lines up for Peel Thunder in Sunday's WAFL grand final against Claremont.
Cox hasn't played since injuring his calf in the final-round loss to Carlton on August 22.
The key back had also been battling some niggles a month earlier, but there was hope he would be 100 per cent fit to take on the Swans after making it through main training on Tuesday.
However, given Cox's limited lead-in to the match, coach Justin Longmuir told the 28-year-old later on Tuesday that he won't be on the plane to Sydney.
"He got through the training session well. Unfortunately, though, he won't make the trip," Longmuir told SEN.
"We feel like he's in a good spot. He couldn't have done much more.
"It's just going into a prelim, in his position, it's a really tough ask, so he'll stay behind and play Sunday and, like I said to him yesterday, next week will be next week."
Longmuir praised the way Cox took the bad news.
"I always do those meetings one-on-one, so it's less confronting for the player," Longmuir said.
"He took it really maturely. He understood.
"He's a player that takes a little bit of time to get his fitness back. He's a bit of a cramper, so he understood that going into a prelim would be a big challenge for him.
"He was disappointed, but he's such a mature person and a guy of great character, so he understood what's ahead of him, and he won't give up any hope of us winning and him playing next week."
If all goes well for Cox, he will snare a WAFL premiership with Peel Thunder on Sunday, before collecting an AFL flag with the Dockers six days later.
Cox's absence against Sydney means Alex Pearce and Oscar McDonald will again take the two key defensive posts, with help from Heath Chapman or Luke Ryan as Fremantle's third "big''.
Longmuir says he will bring a squad of 25 across to Sydney, meaning there will be two emergencies.
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