The hosts could recapture the Ashes with victory at the WACA after dominant wins in the opening two tests in the five-match series in Brisbane and Adelaide but Faulkner, 12th man in those contests, will not be part of it.
The all-rounder broke the thumb on his right hand in Thursday morning's net session and Cricket Australia later confirmed he would miss the match.
"James was struck on the right thumb while batting in the nets and was subsequently taken for an X-ray which revealed a fracture of the thumb," team doctor Peter Brukner said in a statement.
"His progress will be monitored for a return to playing duty depending on how quickly the injury heals."
While a blow to Faulkner, coach Darren Lehmann had already suggested Australia would be sticking with the team that played in the first two tests.
The one flaw in that plan was Harris's knee problem, even if it did not stop him bowling in the nets on Thursday.
"I'm hopeful that everyone will come up, I think there's the obvious one in Ryan-o, who bowled today, and we'll see how he pulls up," Clarke told reporters at the WACA.
"I'm confident he'll be fine."
Faulkner was the most obvious replacement for Harris should the 34-year-old fail to prove his fitness but Australia also have seamers Doug Bollinger and the uncapped Nathan Coulter-Nile on standby.
"I think one of those three will come in and replace Ryan if he's not fit but, as I say, I'm very confident that Ryan will be okay," Clarke said before the results of Faulkner's scan were made known.
Despite the success Australia's pace bowlers - Mitchell Johnson in particular - have enjoyed so far in the series, Clarke said he would be unlikely to send England in to bat if he won the toss for the third straight test.
"I find it extremely hard to send the opposition in for a test match," he said.
"I'll see what the conditions are like tomorrow. I've always looked at batting first in a test match because you give yourself the opportunity to win the game.
"Unless the wicket is extremely green, I'd find it hard to send a team in."
Clarke scored a century in both the 381-run first test victory in Brisbane and the 218-run victory in Adelaide and said he thought the Perth wicket, for all its bounce, would offer plenty of runs as well.
"It's always hard to start, particularly in Brisbane and Perth, and bowlers can get on a roll," he said.
"But once you get a start, Perth, like Brisbane, is as good a place to bat as anywhere in the world because you've got consistent pace, consistent bounce and a quick outfield.
"The wicket looks as good a wicket as a I've seen in Perth for a long time. So I think we're going to see another tough test match that will go five days."