Kepler Bradley was also preferred over Jon Griffin, while Matt de Boer was an automatic inclusion after his rest last week.
Youngster Tom Sheridan made way for the hard-nut midfielder’s return.
The emergencies, who all travelled to Melbourne, were Dylan Roberton, Cameron Sutcliffe and Zac Clarke.
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Senior coach Ross Lyon said Silvagni was in the side not to replace McPharlin, but to add something in his own right.
“We are not going to replace Luke specifically,” Lyon said
“We just want Alex to be himself, not play like Luke. Just give great effort. I’m sure he will be fine.”
Geelong, spearheaded by Tom Hawkins, leads the league in marks inside 50 this season, and Lyon said it would be on the entire Freo team, not just the defence, to help contain them on Saturday night.
“It’s a strong feature of their game, they average about 15 (marks inside 50) a week,” he said.
“It’s about pressure up the field. They tend to pass it in very well so we’re going to have to pressure the ball carrier and try and not fight individual battles.”
On replacing Griffin with Bradley, Lyon said it had been the club’s preferred model all season to go with a ruck/tall-forward combination in favour of two ruckmen.
“We really liked a bit of what we saw from Jon, but we would have liked more of it,” he said.
“Going forward it’s something we’re keen on but it certainly needs more practice.”
The Cats are among the best sides in the competition at transferring the ball from defence into attack, particularly during the past six weeks.
“I think that’s about pressuring them and stopping their outlets,” Lyon said.
“Look, they are a proven premiership team, triple premiership players the majority of them.
“It would be great to announce ourselves on the big stage.”
A coach in three AFL Grand Finals, Lyon had a chat with the team on Wednesday about what to expect come Saturday.
“I just told them finals are about the basics. You’re all going to be a little bit nervous, but focus on what you need to do and you’ll be fine.”
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