The national selection panel says the all-rounder will not be part of the squad in Brisbane on Friday, but will link up with the team in Sydney ahead of the third one-day match.
Coach Darren Lehmann says selectors are looking to give Watson a break, in the same way they have done with Mitchell Johnson, who missed the opening one-day in Melbourne.
Meanwhile, James Pattinson and Aaron Finch have been released to play for the Melbourne Renegades on Tuesday.
"Both James and Aaron will play for the Renegades, neither of these players have been involved in the Ashes Series so their lead in to this ODI Series has not been as intense," Lehmann said.
Pace bowlers Johnson, James Faulkner, Clint McKay, Nathan Coulter-Nile and batsman Shaun Marsh will travel to Brisbane on Tuesday, while the remainder of the squad, including Pattinson and Finch, will arrive the following day.