Joe Root, Alex Hales, Moeen Ali and Mark Wood also return for the tie with Pakistan at Old Trafford on 7 September after missing Sri Lanka in July.
Liam Dawson, Chris Woakes, James Vince, and Dawid Malan all miss out.
However, rapid T20 specialist Tymal Mills retains his place.
Stokes missed the tie against Sri Lanka, which England won by eight wickets, but has figured in the ongoing five-match ODI series, in which they have beaten Pakistan in the first three fixtures.
England impressed at Trent Bridge on Tuesday, scoring an international ODI record 444-3.
Hales scored 171 in that match, the highest score by an England batsman in limited overs cricket, while Root added 85 - his fifth consecutive ODI half-century.
Liam Dawson took 3-27 on debut against Sri Lanka, but misses out as Test spinner Ali returns, while Malan drops out of the squad without making his debut.
National selector, James Whitaker, said: "It is excellent to see the progress we are making in white ball cricket across both formats.
"It is testament to the excellent work being nurtured in the county structure and through the England Lions, that there is a depth of quality pushing the nucleus of the current group."
England Twenty20 squad: Eoin Morgan (Middlesex), Moeen Ali (Worcestershire), Sam Billings (Kent), Jos Buttler (Lancashire), Alex Hales (Nottinghamshire), Chris Jordan (Sussex), Tymal Mills (Sussex), Liam Plunkett (Yorkshire), Adil Rashid (Yorkshire), Joe Root (Yorkshire), Jason Roy (Surrey), Ben Stokes (Durham), David Willey (Yorkshire), Mark Wood (Durham)

Ming Jiang, 43, was in debt and being chased by creditors but his friend and fellow Chinese national Yang Liu, 36, could afford to gamble, the jury heard.
It is alleged Mr Jiang, of Beswick, dumped the suitcase in a remote Derbyshire lay-by and set it alight.
Mr Jiang denies murder. His trial at Minshull Street Crown Court continues.
Peter Wright QC, prosecuting, told the jury that Mr Jiang murdered Yang Lui as "a solution to his financial problems".
"He was a heavy gambler and, like many gamblers, lost more than he won," Mr Wright said.
"He dismembered the body - in all likelihood in his own flat - and then disposed of the body parts.
"He then set about assuming the dead man's identity, gaining access to his bank accounts and his personal effects and his apartment."
A total of Â£800 was taken from the dead man's bank account, the jury was told.
Mr Wright told the court Mr Liu's body was badly burned and had been extensively dismembered.
His head, both lower arms and both lower legs had been severed by "some bladed form of weapon" and removed, he said, adding: "They have never been found."
The jury heard the victim was last seen alive "in the vicinity" of the defendant's flat on 5 October 2016.
Using CCTV footage, detectives identified a silver Mercedes approaching and leaving the lay-by where the suitcase was dumped, just off the A628 at Tintwistle.
They discovered it was registered to Mr Jiang.
Distinctive tyre tracks also fitted the car, while traces of blood in the boot matched DNA from Mr Liu's body, the court was told.
The trial continues.
Ben Stokes has returned to the England Twenty20 squad for the first time since being hit for four sixes in the final over of the World T20, when West Indies beat England.
[NEXT_CONCEPT]
A prolific gambler murdered his wealthy friend to solve debt problems then dismembered his body and stuffed it into a suitcase, a court has been told.