Kusal has still not recovered sufficiently from a hamstring injury that he picked up in July while Binura still has a issue with his back from last month.
Both players were initially named in the squad for the but will now be replaced by Pavan Rathnayake and Dilshan Madushanka.
The update to the squad means Charith Asalanka, who had returned to the vice-captain's position for the series, will now lead Sri Lanka in the shortest format in England.
Asalanka returned to the leadership group three months after being deposed as ODI captain and six months after being sidelined from the T20I unit.
The three-match T20I series in England will start on 15 September in Southampton with further matches in Cardiff and Manchester, while the teams will then contest a three-match ODI series.
Sri Lanka T20I squad: Pathum Nissanka, Kamil Mishara (wk), Lahiru Udara (wk), Kamindu Mendis, Charith Asalanka (captain), Janith Liyanage, Pavan Rathnayake, Dasun Shanaka, Dunith Wellalage, Wanindu Hasaranga, Maheesh Theekshana, Tharindu Rathnayake, Dushmantha Chameera, Eshan Malinga, Nuwan Thushara, Dilshan Madushanka
Kusal Mendis has been confirmed as the new Test captain of Sri Lanka after Dhananjaya de Silva stepped down from the position to leave leadership duties "to the next generation".
Tom Banton marked his return to England's one-day side in style, smashing his maiden international century as England thrashed Sri Lanka by 223 runs at The Oval.
Kusal Mendis produced a superb century as Sri Lanka bounced back from their opening ODI defeat to beat England by 16 runs at Headingley and level the three-match series at 1-1.
England continued their dominance over Sri Lanka with a comfortable 89-run victory in the first ODI at Chester-le-Street as spinner Will Jacks picked up his maiden five-wicket haul.
