"Ryan bowled today so we're going to have to wait and see how he pulls up," Clarke said. "I'm confident he'll be fine."
Harris bowled at full pace in the nets on Thursday and didn't appear to be troubled by the knee soreness.
The 34-year-old fast bowler has struggled with injuries throughout his career, limiting him to 18 tests, but he has become a key member of Australia's pace attack by taking 32 wickets in his past six tests.
Australia had put pace bowlers Doug Bollinger and Nathan Coulter-Nile on standby.
Clarke has announced his lineup the day before each of the first two tests but was more cautious in Perth, where Australia is hoping to take a 3-0 series lead and reclaim the Ashes.
"I'm going to wait until the toss and see how everybody pulls up after training and it gives us another opportunity to have a look at the wicket," he said.
If all players are fit, Australia is likely to retain the same XI that produced lopsided wins in the first two tests in Brisbane and Adelaide.
Johnson has taken 17 wickets in the first two tests and is expected to trouble the English batsmen again on a pitch renowned for its pace and bounce.
Clarke will be playing his 100th test and is hoping to celebrate the milestone by taking an unassailable lead in the five-test series.
"That's why it's most special for me. The fact that we have a chance to win the Ashes," he said. "It's fantastic that I've been able to play 99 test matches for my country."