In-form top order batsman Jos Buttler was rested from the one-off ODI against Scotland in Edinburgh on June 10.
Buttler, however returned to the 14-player group, replacing Sam Billings with speedster Tom Curran also being selected for the five-match series against Australia beginning at The Oval on June 13.
The inclusion of all-rounder Ben Stokes will also bolster the home side, who supplanted India at the No.1 ODI team in the ICC's rankings in April following the annual rankings update.
Skipper Morgan, who fractured the ring finger on his right hand while fielding for Middlesex against Somerset and will not play for the World XI in Thursday's charity Twenty20 game against the West Indies at Lord's, is confident of returning to take on Australia.
"It's not a huge concern, it's one that hopefully we can manage past about a week when the swelling goes down," Morgan said.
"It's not fractured into the joint, which is a really good result. I'll be fine for the one-dayers.
"I will hopefully be back for one more Middlesex game, potentially two. We will wait and see," he added.
England squad for Scotland: Eoin Morgan (Captain), Moeen Ali, Jonny Bairstow, Sam Billings, Alex Hales, Liam Plunkett, Adil Rashid, Joe Root, Jason Roy, Ben Stokes, David Willey, Chris Woakes, Mark Wood.
England squad for Australia: Eoin Morgan (Captain), Moeen Ali, Jonny Bairstow, Jos Buttler, Tom Curran, Alex Hales, Liam Plunkett, Adil Rashid, Joe Root, Jason Roy, Ben Stokes, David Willey, Chris Woakes, Mark Wood.
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