Lobb was hurt in a marking contest in the third term of the 24-point win and exited the game in the final term. The 29-year-old originally hurt his shoulder back in Round 19 but has been playing though the pain, according to Longmuir.
"We know the injury. He's been carrying it for three weeks. He just got a stinger on it and couldn't go on tonight," the Freo coach said post-match.
"But we think he'll be alright after seven days, hopefully.
"I'm proud of his efforts after he got injured to halve some contests and remain in the game and keep working his way through it.
"When you see a player out there carrying an arm, you just want to protect them. That's why we subbed him out. He's a fast healer … so fingers crossed he gets up."
Though the tall forward is expected to be right to feature in Round 23, and Fremantle's finals plans, Longmuir conceded that he may be playing through pain, as he has been for the past few weeks.
"He's pretty good at it to be honest," Longmuir said.
"He doesn't let on when he brings injuries into games and he pushes through it really well.
"But when we saw him carrying that arm a bit we just thought it was best to get him out of there."
Fremantle's win against their cross-town rivals has secured a home final and kept their top four hopes alive with just one full round remaining in the home and away season.
The Dockers may be bolstered by the inclusions of one of their stars for their final regular season game too, with Longmuir admitting that skipper Nat Fyfe was nearing a return.
"We were holding him back this week so we're pretty confident he'll get up next week," Longmuir said.
"If not, we've got a bye and a WAFL game during the bye, so we'll look at that."