Durham all-rounder Stokes was dropped for Wednesday's fourth ODI against West Indies at The Oval after being arrested early on Monday in Bristol following England's win in the third ODI in the southwest city on Sunday.
The 26-year-old remains under investigation after being released without charge.
England national selector James Whitaker later told the BBC that Stokes would remain in his position of vice-captain to Test skipper Joe Root.
The squad contained three uncapped players in 23-year-old Somerset fast bowler Craig Overton, 20-year-old Hampshire leg-spinner Mason Crane, who will provide spin support to Moeen Ali, and Surrey wicket-keeper Ben Foakes, 24, included as cover for first-choice gloveman Jonny Bairstow.
Meanwhile, there were recalls for middle-order batsmen James Vince and Gary Ballance despite the pair's struggles during their previous Test stints.
Essex batsman Tom Westley, who failed to convince at number three during this season's home series against South Africa and West Indies was dropped, while there was no recall for Durham paceman Mark Wood.
Toby Roland-Jones was ruled out following the Middlesex seamer's recent stress fracture of the back.
Ashes-holders England are due to travel to Australia on October 28, with the first of five Tests against their arch-rivals set to start in Brisbane on November 23.
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