Cricket Australia has opted to give the left-armer time off after he took 37 wickets to be named man of the series during to 5-0 Ashes whitewash.
National selector John Inverarity said: "Mitch has had a brilliant summer with the Test side and while he is a crucial member of the ODI squad it is important that he has a bit of a break now.
"The (National Selection Panel) will be looking to provide a break, also, for most of the players in the ODI squad who played in the Tests against England."
Australia coach Darren Lehmann confirmed that Johnson would return for the second ODI in Brisbane on January 17.
"He'll play in Brisbane, definitely," he said.
"It's one of his home towns so he'll play there.
"It's obviously been a very big summer for him.
"So we'll just give him a short little break and make sure he's getting fresh for the other one-dayers.
"It's important that we put the best side that we possibly can out, but understanding that it's been a hectic five Test matches.
"Some of the Test boys especially are weary."
Lehmann ruled out the possibility of resting a number of first-choice players in the same game as he looks to start building towards a home World Cup in 12 months' time.
"We'll sum it up as we go. We certainly don't want to go down the path we have previously where we've rested clumps of players," he said.
"We certainly want to pick and choose when we do it (rest players). We want them to play in their home state.
"We want to make sure we put together a good squad looking ahead to the World Cup.
"This one-day format is very important for us.
"It give some guys and opportunity that we think are going to get to the World Cup."