McGlynn suffered a hamstring strain in Sydney's qualifying final win over Adelaide on September 8 and was in tears on the bench at AAMI Stadium.
But despite hopes the former Hawk would be available for the meeting with the Magpies, Swans physio Matt Cameron said he had been ruled out.
"It's about eight or nine days now since he was injured and things are progressing along," Cameron told the club's website.
"He's not going to be available this weekend, unfortunately, but he is making progress and we will reassess things on the weekend.
"At this stage he's not ready to team train and that makes him unavailable."
McGlynn remains a chance to play in the grand final should the Swans make it to the decider on September 29.In other injury news at the Swans, Tommy Walsh (leg) and Jarred Moore (groin) are both set to return to training.