Ahead of Friday's second ODI at the Gabba, Bayliss said he was not involved in the decision to bring Stokes back.
Stokes and two other men will appear at Bristol Magistrates' Court following the incident in the early hours of September 25 after England had beaten Windies in an ODI in the city.
Stokes was suspended from global duty by the England and Wales Cricket Board following his involvement in an incident outside a Bristol nightclub in September that reportedly left a man with a fractured eye socket.
Earlier this week the Crown Prosecution Service charged Stokes over the nightclub incident but yesterday the European Central Bank confirmed he would now be considered for selection.
But Stokes has been given permission to return for England in the upcoming series against New Zealand, despite charges hanging over him.
Stokes has not played for his country since his arrest and stated that he was "extremely delighted" to have been given the opportunity to resume his worldwide career in his country of birth. "I can't wait to get back out on a pitch with the three Lions on my chest", his tweet read.
England is now involved in a one-day worldwide series in Australia but the European Central Bank said Stokes is expected to return to England duty for February's Twenty20 matches in New Zealand.
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In defence of Conte's side they have scored 66 goals in all competitions in the 33 matches they have played to date this season, an average of exactly two per game.
Having missed the Ashes series loss, Stokes has now been cleared to resume his global career while he contests a charge of affray following an incident outside a nightclub in September.
His first appearance is scheduled for a match against the Black Caps in Wellington on February 13.
He was suspended from the England team after his initial arrest and subsequently missed England's Ashes series in Australia.
Head coach Trevor Bayliss, however, insists the episode did not distract his players during the Ashes series Down Under, which ended this month in a 4-0 defeat.
An ECB statement read: "Following a full board discussion, in which all considerations were taken into account, the ECB board has agreed that Ben Stokes should now be considered for England selection". "We're happy that he has been made available". "It'll be a hard decision".
Both he and Stokes still face an internal investigation from the ECB's independent cricket discipline commission but that will not begin until the legal process has run its course. When tried on indictment - in the crown court - there is a maximum tariff of up to three years in prison.