Cox was "managed" from Friday night's 70-point western derby win over West Coast due to a knee niggle.
Journeyman Oscar McDonald filled in expertly for Cox as Fremantle kicked 11 goals to one after halftime to secure the 16.16 (112) to 6.6 (42) win.
Cox is one of Fremantle's most important defenders with Longmuir earlier this season even labelling him as probably the most underrated key backman in the league.
The 27-year-old has played 15 games this season and is set to return for next Friday night's blockbuster against the Western Bulldogs at Optus Stadium.
"He just had a little bit of an injury with his knee," Longmuir said of the reason he rested Cox against West Coast.
"We thought (that with a) six-day break, travelled back from Adelaide, it was a good opportunity for him to maybe manage that and hopefully get on top of it leading into the back end of the season."
Longmuir also opted to leave out Hayden Young after the injury-plagued midfielder was struck down by illness.
"If it was a grand final they would have played," Longmuir said of Young and Cox.
"But when Young's had different niggles going on and we've put him out there, it's probably resulted in him picking up another injury.
"So we've just got to be careful the way we manage him.
"He's pretty crook, but yeah, if it was a final or grand final, he would have put his hand up to play, but we made that decision for him."
Fremantle (17-2) are almost certain to snare just the second minor premiership in the club's history.
The Dockers' best win-loss record for a season prior to this year was in that minor premiership-winning campaign of 2015 when they went 17-5, and they are set to smash through that record in the coming weeks.
Although Longmuir is proud of his team's achievements so far this season, he knows it's all about the premiership prize at the end.
"It's equalled most amount of games we've won in a season, it's pretty special," Longmuir said.
"But we've still got a lot of improvement left in us.
"The next four to five weeks give us a good opportunity to work on some of those things. We're still hungry as individuals and still hungry as a team to improve.
"Although I'm happy with where we're at, I'm more excited about what's ahead."
Young gun Murphy Reid added to his growing accolades when the Rising Star winner snared the Glendinning-Allan as best afield for his 26-disposal, one-goal effort against the Eagles.
"When he gets the ball in his hands, something special usually happens," Longmuir said.
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