The pair were named in a 16-man squad, though an European Central Bank statement noted: "Their involvement remains subject to any relevant legal or disciplinary developments in relation to the incident in Bristol in September".
Stokes was in action as his England teammates lost the second Ashes Test in Adelaide, a series he is unavailable for as he still waits to hear if he will be charged after being arrested over a late-night fracas in Bristol in September.
Bayliss admitted Stokes's potential appearance in Australia could be a distraction for the team.
The England v Australia ODI series consists of five matches with the first at the Melbourne Cricket Ground on January 14. "We've got to adjust to that at some stage".
However, Stokes returned to competitive cricket last Sunday after New Zealand's domestic side Canterbury signed the all-rounder as their overseas player.
Stokes' performance was at least an improvement on his Canterbury debut last weekend when he scored only two runs in a six-ball innings and went wicket-less in nine overs in a loss to Otago. He did better against Auckland on Wednesday, hitting 34 from 41 deliveries as he shook off the rust.
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The participation by Stokes and Hales in the series will however stay a subject to any relevant legal or disciplinary developments in relation to the incident in Bristol in September. He is waiting for the judgment from the Crown Prosecution Service (CPS).
Bayliss also said he was ready for all the scrutiny that Stokes's reinstatement would bring.
Police completed their investigation last week and the case is with United Kingdom prosecutors, who are determining whether to charge Stokes.
"The ECB Board has convened via conference call to make the decision after being informed that Hales is deemed a witness and will face no charges".
The news has come as a big relief for the English cricket fans. This follows Police confirmation that he will face no charges and the independent Cricket Discipline Commission staying its disciplinary process.
Kent batsman Sam Billings and Durham seamer Mark Wood were also included in the squad that defeated West Indies (4-0) earlier this year.