All-rounder Tom -- who like Sam plays for the same county side Surrey -- has not recovered from a left side strain and will also miss the three match T20 series with the Indians which begins later on Tuesday.
England batsman Dawid Malan had been called up last Friday as a replacement for him for at least the first of the T20 matches.
"Tom will now commence his rehabilitation programme at the Oval under the supervision of Surrey and England's medical teams," read the ECB statement.
Revised ODI squad:
Eoin Morgan (capt), Moeen Ali, Jonny Bairstow, Jake Ball, Jos Buttler, Sam Curran, Alex Hales, Liam Plunkett, Adil Rashid, Joe Root, Jason Roy, Ben Stokes, David Willey, Mark Wood.
First Published: July 3, 2018, 6:54 PM IST