The 23-year-old has not played since England's one-day series win over India in July, having suffered discomfort in his knee while scoring 91 at Lord's. He had surgery in September and travelled to Australia in anticipation of a return, but a scan has ruled him out of the tour
"Jacob Bethell has been ruled out of the white-ball tour of Australia following a scan on his right knee," the ECB said.
England have called up James Coles and Eddie Jack to the ODI squad as replacements for Bethell and fast bowler Josh Tongue, who was already out with a left big toe injury.
England begin the three-match ODI series on Friday in Australia before playing five Twenty20 internationals. They then travel to South Africa for a test series starting on December 17th.