Williamson opted to miss the recent T20 series against Australia under the terms of his casual contract with New Zealand Cricket, while he is also returning to full fitness after a “minor medical issue”, according to coach Rob Walter.
All-rounder Santner suffered a groin injury while representing Northern Superchargers in The Hundred and has not played since.
Seam bowler Ben Sears will miss the England T20 series because of a hamstring tear, while all-rounder Jimmy Neesham has been included.
After the first two T20s at the Hagley Oval on 18 and 20 October, the series concludes at Eden Park in Auckland on 23 October.
New Zealand T20 squad: Mitchell Santner (c), Michael Bracewell, Mark Chapman, Devon Conway, Jacob Duffy, Zak Foulkes, Matt Henry, Bevon Jacobs, Kyle Jamieson, Daryl Mitchell, Jimmy Neesham, Rachin Ravindra, Tim Robinson, Tim Seifert (wk).
England T20 squad: Harry Brook (c), Rehan Ahmed, Sonny Baker, Tom Banton, Jacob Bethell, Jos Buttler (wk), Brydon Carse, Jordan Cox, Zak Crawley, Sam Curran, Liam Dawson, Jamie Overton, Adil Rashid, Phil Salt, Luke Wood.