With Watson absent, fellow all-rounder Daniel Christian was recalled to the team for the three matches, his first taste of international cricket since being part of the squad for the World Twenty20 event in Sri Lanka in 2012.
"Given Shane's workload in the past 12 months, we consider it would be beneficial for him to have a longer break and continue his training program at home in Sydney ahead of the final ODI and the tour of South Africa," Australia coach Darren Lehmann said.
After completing a 5-0 whitewash in the Ashes series, Australia won the first one-dayer against England in Melbourne at the weekend and will be out to extend their dominance in the second contest of the five-match series on Friday.
The fifth and final match is in Adelaide on January 26.
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