Peter Siddle said his participation in the Test would have risked a long-term injury.
Siddle hit back at criticism of his omission, saying that he might have ultimately hurt his side more.
Following a draining draw in the second Test in Adelaide, Australia took a completely new pace attack to Perth and were crushed by 309 runs to lose the series 1-0.
Siddle took six wickets at Adelaide and emerged unscathed after he carried a huge workload in the absence of injured seamer James Pattinson, but had only three days to recover in time for the final Test at the Western Australia Cricket Association Grounds.
"Obviously I wanted to be out there and doing my best to try and win that game, but after going through what I did in Adelaide, knowing that if I had been the one that got injured … it would have put us out of the game by a long way," the 28-year-old told Wednesday's Fairfax newspapers.
"I think we made the right decision. Instead of missing that one match, it could end up being seven matches – including India."
Australia starts a three-match Test series against Sri Lanka in Hobart next week before heading to India for a four-Test series starting February.
'Injuries deplete bowling stock'
Australia's selectors and fitness staff have come under fire over their player-management, with a glut of injuries depleting their bowling stocks for a second successive home summer.
Young pace bowlers Pattinson and Pat Cummins have both broken down with injuries and are expected to miss the entire Sri Lanka series, while all-rounder Shane Watson missed the first two Tests against South Africa with a calf strain.
Only Siddle has been rated a certain starter by Australia coach Mickey Arthur for Australia's pace attack at Hobart, with fitness queries dogging a number of other candidates along with captain Michael Clarke.
Clarke has been ordered to forgo the first round of the domestic Twenty20 competition after suffering lower back stiffness following Perth, while paceman John Hastings, who made his Test debut at the grounds, may be ruled out of Hobart after suffering back pain, Cricket Australia said on Wednesday.
Workhorse paceman Ben Hilfenhaus was rested for the Perth Test but has also been ordered to miss the T20 "Big Bash" season-opener.
Strategies
Seamer Josh Hazlewood, who was 12th man in Perth, would be rested for up to six weeks after suffering pain in the same left foot that suffered a stress fracture last season, Cricket Australia added.
The injuries leave pacemen Mitchell Johnson and Mitchell Starc strong candidates to retain their places in the side, despite being flayed by South Africa's batsmen in the second innings of the final Test.
"We've got to really discuss our attack as an attack and not in terms of individual bowlers," Arthur said earlier this week.
"We've got to look at what the best attack is for us to get 20 wickets and we need to sit down again and make those decisions." – Reuters