Clarke, all-rounder Shane Watson, wicketkeeper Brad Haddin and opener David Warner were all rested for the fourth one-dayer in Perth, which England won by 57 runs to snap their nine-game losing streak.
Clarke and Watson will return for the fifth and final one-dayer in Adelaide, but Warner and Haddin have been put on ice ahead of next month's three-Test tour of South Africa.
Australia lead the one-day series 3-1 and have little to play for in the final match.
Bailey is glad to hand the captaincy back to Clarke, and defended Australia's decision to rest so many key players in Perth.
"I'm surprised that Pup's actually coming back after just missing one. I thought he might miss two," Bailey said.
"Don't get me wrong, you want to win every game you play.
"But given how crammed the schedule is, if you do get an opportunity to rest a few of the guys, you take the opportunity.
"I don't think any of the players have got an issue with the fact those guys had earned a rest.
"There's some huge series coming up, particularly that Test series in South Africa."
Chasing England's 8-316, Australia were dismissed for 259 despite a sparkling 108 from opener Aaron Finch.
"It was a really mature knock," Bailey said.
The result gave England their first win on tour, and also brought a smile to the face of besieged captain Alastair Cook.
Cook had contemplated giving up the one-day captaincy after his side slumped to a 3-0 deficit in the series.
But he is now determined to lead the side to next year's 50-over World Cup in Australia and New Zealand.
"With what I've learned over the past three years, it would be wrong to change so close to a World Cup," Cook said.
"During the last four or five days, I have done quite a lot of talking to the guys.
"Sometimes you do need a bit of reassurance when you've lost a lot of games on a tour.
"When you chat to some guys you trust and respect, and find out what they're thinking, it gives you the confidence (to go on)."
Cook praised the performance of all-rounder Ben Stokes, who scored 70 with the bat before snaring four wickets in a man-of-the-match performance.
Stokes has established a love affair with the WACA after scoring his maiden Test century there in December.