New Zealand's regular skipper Williamson and paceman Boult will return home for pre-planned rest after the conclusion of the two-match Test series, which hosts Sri Lanka are leading 1-0.
The squad will be led by fast bowler Tim Southee, and features three specialist spinners in Ish Sodhi, Mitchell Santner and Todd Astle.
New Zealand selector Gavin Larsen said that after an impressive ICC Men's Cricket World Cup 2019 campaign, the team would now shift focus to the next ICC tournament, the ICC Men's T20 World Cup 2020, prior to which the Blackcaps are scheduled to play nine T20I series.
"Following that amazing ride in the ODI World Cup, it’s exciting to begin setting our sights on another world event,” Larsen said. "The series in Sri Lanka will be a challenging one against a team who are tough to beat in their own conditions.
"Our T20 team has been pretty consistent over the past couple of years and we’re really happy with the power and versatility we have in this squad. Kane and Trent played an enormous role in our recent World Cup campaign and with a big summer ahead, we see it as a good opportunity to give them a rest."
New Zealand T20 Squad for : Tim Southee (c), Todd Astle, Tom Bruce, Colin de Grandhomme, Lockie Ferguson, Martin Guptill, Scott Kuggeleijn, Daryl Mitchell, Colin Munro, Seth Rance, Mitchell Santner, Tim Seifert (wk), Ish Sodhi, Ross Taylor.