As well as Cook, England have left out Stuart Broad, Ian Bell, James Anderson and Graeme Swann from their party for the lone one-day international against Ireland and the five-match one-day series with Australia that follows. (Agencies)
However, star batsman Kevin Pietersen has been included in the squad for the Australia series, with fellow Ashes-winning batsmen Joe Root and Jonathan Trott also set to face England's arch-rivals in the one-day format after they too were excused the trip to Dublin.
Former Ireland international Eoin Morgan will captain the side in the absence of Cook and Broad, with the squad including five uncapped players in pacemen Chris Jordan and Jamie Overton as well as Morgan's fellow ex-Ireland star Boyd Rankin.
Meanwhile batsmen Michael Carberry, a key figure with the successful Hampshire county one-day side, and Yorkshire's Gary Ballance will also look to win their first ODI caps.
With Australia's 18-man squad containing just seven players who took part in the Ashes, it is clear both countries are looking ahead to the return Ashes series in Australia starting in November.
England begin their tour with a three-day match against Western Australia starting on October 31, meaning leading players will have little time for a break after a packed home schedule followed back-to-back tours of India and New Zealand.
Cook, Anderson, Bell, Broad and Swann were all involved -- Pietersen was injured in the early part of the English season -- as England won a home Test series against New Zealand, reached the final of the Champions Trophy and retained the Ashes with a 3-0 win over Australia in a five-match series concluded with a dramatic draw at The Oval on Sunday.
This latest squad announcement means Cook -- who does not play Twenty20 international cricket -- has been rested from a squad for the first time since he took over the Test captaincy a year ago.
England and Australia will next meet in a separate two-match Twenty20 series, where the hosts will be captained by Broad and Australia by George Bailey rather than Test skipper Michael Clarke, in fixtures at Southampton and Durham on Thursday and Saturday respectively.
England ODI squad vs Ireland:
Eoin Morgan (capt), Gary Ballance, Ravi Bopara, Danny Briggs, Jos Butler, Michael Carberry, Steven Finn, Chris Jordan, Jamie Overton, Boyd Rankin, Ben Stokes, James Taylor, James Tredwell, Luke Wright.
England ODI squad to play Australia:
Eoin Morgan, Ravi Bopara, Jos Buttler, Michael Carberry, Steven Finn, Chris Jordan, Jamie Overton, Kevin Pietersen, Boyd Rankin, Joe Root, Ben Stokes, James Tredwell, Jonathan Trott, Luke Wright.
As well as Cook, England have left out Stuart Broad, Ian Bell, James Anderson and Graeme Swann from their party for the lone one-day international against Ireland and the five-match one-day series with Australia that follows.