Black Caps coach Gary Stead said the withdrawals were grounded in fresh medical advice.
“We want both Kane and Kyle to be in the best possible place leading into the next block of test cricket against South Africa and Australia,” he said.
“Based on discussions with the medical staff and the players it was decided a period of rehabilitation and conditioning was the best option for both of them.”
Stead said Ravindra, with 18 T20I appearances, and Duffy, with 10, provided strong additions to the squad mix for Bangladesh.
“Jacob is an experienced T20 cricketer and always brings a lot when he is part of the Black Caps environment. He’s worked very hard on his white-ball skills in recent seasons.
“Rachin adds to any environment he’s a part of and has a great desire to learn and develop his game - across all three formats.”
Mitchell Santner will be captain for the series in Williamson’s absence. Santner has led the team 14 times previously across the two shorter formats.
The T20 squad will assemble in Napier on Boxing Day.
Revised Black Caps T20 squad to play Bangladesh:
Mitchell Santner (c), Finn Allen, Mark Chapman, Jacob Duffy, Adam Milne, Daryl Mitchell, James Neesham, Glenn Phillips, Rachin Ravindra, Ben Sears, Tim Seifert, Ish Sodhi, Tim Southee.
Listen to ball-by-ball commentary of every Black Caps match this summer live and free on iHeart Radio with The Alternative Commentary Collective.