Buttler made four and nought as Australia won the first two one-dayers and England's management have decided to rest him ahead of the three-match test series against Pakistan in the United Arab Emirates starting next month.
"It has become clear in the last couple of days that Jos will benefit from a break from cricket ahead of the winter tours," England coach Trevor Bayliss told reporters on Sunday.
"While we initially felt Jos would have enough left in the tank, rest is key and Jos has had a heavy workload throughout 2015."
Bairstow was called into the test team in place of Gary Ballance after England lost the second match of this year's Ashes series, making 74 to help his side win the fourth game at Trent Bridge and win back the urn.
Buttler, 24, failed to make a half-century in five tests against Australia and has not fired with the bat since scoring a brilliant 129 in the first one-day international against New Zealand at Edgbaston in June.
England, who triumphed 3-2 in the Ashes, must win the last three one-day internationals, starting at Old Trafford on Tuesday, to deny the world champion Australians victory in the one-day series.
(Reporting by Ed Osmond; editing by Justin Palmer)
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