The Asian Cricket Council (ACC) selector from Pakistan, Mohsin Khan, said Shoaib had not made a complete recovery from the knee injury that had restricted him to just one Test and four one-day international appearances in the last 14 months.
A Pakistan Cricket Board official said that Mohsin told the PCB that Shoaib would be replaced in the Asia squad.
"After a lot of consideration we felt Shoaib still needs time to regain full match fitness. So we didn't want to take a risk with him at this stage," former Test player Mohsin told Reuters on Tuesday.
The three series between representative sides from the two continents is being played in Bangalore and Chennai starting from June 6.
The Asian side has been picked by the ACC selection committee made up of nominees from all four Asian Test-playing nations; India, Pakistan, Sri Lanka and Bangladesh.
The selectors originally named Shoaib in a 14-member squad to be captained by Mahela Jayawardena of Sri Lanka, and includes Pakistan's Mohammad Yousuf and Mohammad Asif.
"We have some very important Test series coming up and we want Shoaib to be fit in time for them. That is why the consensus is he should not be risked," the PCB official, Dr Ehsan Malik said.
The 31-year-old Shoaib, who has taken 169 Test and 208 one-day wickets has struggled with fitness problems since appearing in the Karachi Test against India in February 2006.
He and fellow paceman Asif tested positive for the banned steroid nandrolone last October and were recalled from the Champions Trophy in India.
The pair were initially banned but reinstated following an appeal.
Pakistan plays South Africa in Sept-Oct and then tours India before hosting Australia for three Tests early next year.
Shoaib had earlier opted out of the Afro-Asia Cup citing family commitments but than made himself available saying he had made a satisfactory recovery from injury.