Selectors opted to rest Clarke, David Warner, Brad Haddin and Shane Watson from Friday's one-day international in Perth, which Australia lost to England by 57 runs, ahead of next month's highly anticipated Test tour of South Africa.
But Clarke and Watson are set to return to the side on Sunday despite Australia having already wrapped up the five-match ODI series.
Should Clarke take to the field in Adelaide, it will mean he played in all five Tests and four of the five ODIs of the home summer, but would also have had little time to rest his temperamental back problem.
Haddin, Warner and Mitchell Johnson will not play in Adelaide.
Bailey, who has captained Australia 13 times in ODIs for just four wins, felt Clarke was entitled to a longer rest so he was primed for the tour of South Africa.
"I don't think any of the players have got an issue with the fact those guys had earned a rest," Bailey said.
"But I'm surprised that Pup's (Clarke) actually coming back after just missing one. I thought he might miss two, as far as the job being done of winning the series.
"You want to win every game that you're playing, don't get me wrong, but given how crammed the schedule is, if you do get an opportunity to rest a few of those guys, you take the opportunity, as England have done with some of their key players."
Australia's second-string batting line-up will be eager to bounce back in Adelaide after failing to fire in Perth.
In-form opener Aaron Finch (108) scored his second century of the series, but he received little support from Bailey (11), Shaun Marsh (15), Matthew Wade (23) and Steve Smith (19).
The large victory target of 317 proved too great for Australia and enabled the tourists to register their first international win of the summer.
England scored 93 runs from the final 10 overs, with Jos Buttler (71 off 43 balls) making Australia's wayward bowlers pay.
"One of the areas we highlighted at the start of the series ... is nailing our death bowling," Bailey said.
"I generally think our one-day cricket is in good order. It's really hard to be good at the death at the moment, particularly when you're playing against a side who have batters (settled).
"We have some bowlers who are going to be really, really skilled at it in James Faulkner and Nathan Coulter-Nile, but it's just a matter of nutting out their plans really clearly to each batter and also working out how they best bowl at the death.
"They got more than I hoped, but I thought it was a score we could chase down."