The 'A' tour is designed to give promising young players an introduction to international cricket.
However, South African-born Pietersen recently starred during England's One-day tour of South Africa where he scored 454 runs, including three hundreds, at an average of over 151.
David Graveney, England's chairman of selectors, said: "Following Kevin's outstanding performances in South Africa, the selectors have decided to withdraw him from the England 'A' tour party which departs on Wednesday, February 23.
"We believe that this decision is in Kevin's and England's best interests and he will now undertake pre-season training with his new County, Hampshire.
"This break will also ensure that he is able to fully recover from a minor hamstring strain before playing further competitive cricket.
"He will be replaced in the tour party by Alistair Cook and this will give Alistair valuable experience against high quality opposition in the sub-continent."
Essex batsman Cook, 20, flew out to India on Sunday as part of his County's contingent taking part in a two-week training camp at the World Cricket Academy in Mumbai.
Commenting on his call-up, Cook told Essex's official website www.essexcricket.org.uk: "I have to say it was a surprise, but a very pleasant one. This is a great opportunity for me. I've already spent time with most of the 'A' team in Perth - apart from Richard Dawson and Vikram Solanki - so I'll be ok."
England lost their One-day series in South Africa 4-1.
The tall, powerful, Pietersen, 24, as well as impressing with his batting also showed a good temperament to cope with the sustained verbal abuse he received from South African crowds angry that he opted for England, his mother's country, because he believed his progress was being blocked in his native land by a racial quota system.
He made his international debut in the One-day series against Zimbabwe last November.
Not originally picked for the South Africa leg of the tour, he was added to the current squad following impressive performances in Zimbabwe.
But now, ahead of Australia's Ashes tour of England later this year, Pietersen is being spoken of as a Test batsman.
"This is a boy who likes a contest, and with the Australians coming, it's pleasing to see there's someone who likes to take people on," said England coach Duncan Fletcher.
Pietersen quit Nottinghamshire, his first English County, in October to join Hampshire and will gain some idea of what an Ashes contest means from Australia leg-spinning great Shane Warne, his new side's captain.