McMahon, 15, has been a goalscoring revelation in recent weeks while fringe Matilda Roestbakken had overcome a torrid run of foot injuries in recent years to register 15 appearances this campaign.
But Roestbakken failed to recover from a foot injury suffered in the first leg of City's semi-final win over Newcastle, while McMahon is on the verge of a stress fracture.
The club is unwilling to risk either player for Saturday's decider against Sydney FC at AAMI Park.
"Unfortunately Shelby will also be out for this weekend," coach Dario Vidosic said.
"So we've had to take her out for the weekend, she's bitterly disappointed as any footballer would be regardless of age.
"But look, everyone else is fine. We've trained normally."
The pair of injuries are just the latest setbacks City have dealt with.
Star forward Holly McNamara went down with an ACL tear early in the season while Matildas utility Kaitlyn Torpey and goalkeeper Lysianne Proulx both sealed transfers to the NWSL.
But Vidosic says the extension to a 22-game, full home-and-away season allowed City to figure things out on the run and recover to win the premiership, his first silverware as a senior coach.
"People forget, we lost Holly in round five, who was probably for me, the best player in the competition, or one of, arguably," he said.
"Then throughout losing her, Wilky (Hannah Wilkinson), other injuries, then to have players get sold in the middle - which was fantastic for the women's game that we could break the (transfer) record twice and see girls achieve their dreams as well to play overseas.
"But overall it (the extended season) gives you that chance where it's not just a short season where three or four games could make the difference.
"So here you can tweak things, find solutions to problems that arise and at the end I think now we're in a good place, and we're really confident for Saturday."
Vidosic, who took over from father Rado partway through last season, has relished the steep learning curve.
"Look, we still continued to play our way," he said.
"So we just had to adapt a few little things, and maybe a few players changing their roles slightly.
"But we still carried on normally as we would. It took us maybe a little bit of time because we had to change so many things.
"Throughout the season, every team sort of ebbed and flowed, but I think overall us and Sydney have been the two that have managed that the best. And now we meet on the final day."
