The end of Pietersen's international career, announced last week, is the latest bombshell to hit English cricket following their 5-0 Ashes trouncing in Australia.
Former Hampshire captain Warne backs Andy Flower's decision to resign as team director, but not the enforced retirement of Pietersen.
The England and Wales Cricket Board cited an issue of ''trust'' as the reason for severing ties with their South Africa-born all-time record runscorer.
In his Daily Telegraph column, former Australia great Warne struggles to understand why captain Alastair Cook would not want a proven world-class match-winner on his side to try to revive English fortunes.
''Cook's captaincy was terribly exposed in Australia, and now he has dumped the best player in the team,'' said Warne.
''It is an incredible decision. Surely as captain you want the best player on your side to help you rebuild.''
Warne believes it is down to all parties to establish and maintain a working relationship.
''Respect goes both ways. It has to be earned by actions.
''The test of a captain is to embrace everyone, especially the mavericks such as KP.
''If I was Cook I would have grabbed KP and said: 'It is you and me buddy. We are going to reshape this team'.
''Cook should ask himself these questions: 'Is KP going to win us games of cricket? Yes. Are we a stronger team with him in the side? Yes.'
''But instead English cricket has dumped Pietersen, and his exit has been handled very badly.
''There have been leaks, statements and pettiness. It has sounded immature and like a primary school playground ... get out of the playground and start acting like grown-ups.''
England, in Warne's estimation, will find life tougher rather than easier without Pietersen.
''I just don't understand why a captain would not want a match-winner in the side,'' he added.
''You can replace a coach, but it is hard to find match-winners. England may discover just how hard as they try to replace Pietersen over the next few years.''