England selectors on Tuesday named left-hander Morgan as the skipper for the single ODI against Ireland to be held on September 3 and the five-match series against Australia starting on September 6 at home.
James Anderson, Ian Bell, Stuart Broad and Graeme Swann, who were part of the Ashes winning team, were also rested for ODIs.
Pace bowlers Chris Jordan and Jamie Overton, Michael Carberry, Gary Ballance and Boyd Rankin are the newcomers.
National selector, Geoff Miller, said: "Following a very intense period of cricket this summer we have decided to rest a number of senior players which will allow them to recover from a heavy workload over the last three months and to prepare for the tour of Australia which begins in eight weeks.
"This creates an excellent opportunity for players who have impressed in county cricket and for England Lions recently to test themselves at international level as we continue to build a squad ahead of the ICC Cricket World Cup which is less than 18 months away.
"There are a number of very experienced one day players in the squad alongside players who are new to international cricket and we are expecting a very tough challenge both from a strong Ireland side and then from Australia in what will no doubt be a very competitive NatWest series."
England ODI squad Vs Ireland: Eoin Morgan (captain), Gary balance, Ravi Bopara, Danny Briggs, Jos Buttler, Michael Carberry, Steven Finn, Chris Jordan, Jamie Overton, Boyd Rankin, Ben Stokes, James Taylor, James Tredwell, Luke Wright.
England squad for ODI series Vs Australia: Eoin Morgan (captain), 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.