"It does feel like the end of some type of era. We might have to take a little more pain before we have sustained success again.
"And we might have to ask for a little patience in that regard over the coming months."
Flower wouldn't discuss exactly who would feel the pain, but the crosshairs will almost certainly land on 33-year-old Pietersen and 31-year-old wicketkeeper Matt Prior.
England have five months before they host Sri Lanka for a two-test series, by which time a full review into the Australian debacle will have been completed.
One thing is certain - Flower has no intention of walking away from his post, and he believes Cook is the right man as captain to lead England out of their funk.
"I'm not going to discuss individuals, but looking at it a little more holistically, I think it will be the start of something new," Flower said.
"I think Alastair Cook as captain can lead that renewal and rebuilding [of] the England cricket side."
- AAP