The opening batsman was dropped from the side for the opening two Ashes Tests, but was recalled at Old Trafford and went on to score 138 runs at an average of 23 for the remainder of the series.
Darren Lehmann has admitted that Warner's recent form, particular in the 50-over format, has been below par and the Aussie coach instead has opted for alternatives such as Phillip Hughes and Aaron Finch, who scored a record-breaking century in a T20 international against England on Thursday.
Lehmann told reporters: "David has been left out of the Australian ODI squad for this tour purely due to his recent lack of form in this format.
"By his own admission, David would acknowledge that unfortunately he hasn't scored the weight of runs that he would like recently in one-day cricket for his country.
"Like all selection matters, it was a tough decision, but like all players he understands the situation and knows he needs to get back to playing RYOBI Cup and making a heap of runs that we can't ignore."
Left-arm seamer Mitchell Starc will take no part in the series, which begins at Headingley on Friday, after returning to Australia to receive treatment for a back injury.
Australia squad: Michael Clarke (capt), George Bailey (vice-capt), Fawad Ahmed, Nathan Coulter-Nile, James Faulkner, Aaron Finch, Josh Hazlewood, Phil Hughes, Mitchell Johnson, Shaun Marsh, Glenn Maxwell, Clint McKay, Adam Voges, Matthew Wade, Shane Watson