The club announced Shamir's decision on Wednesday.
"Dan led us through the most difficult two years in Breakers' history and through circumstances that no other basketball team in the world had to go through," Breakers owner Matt Walsh said.
"His work ethic and professionalism are a model for all, and I am very thankful for the last three years."
In his place, current assistant coach Mody Maor has been elevated to head coach – a move that was already in the works at Breakers HQ.
Walsh said the team had been planning for Maor to take over from Shamir at the end of the latter's contract, with the 36-year-old set to lead the club in their return to New Zealand shores next season.
"Ask the players; they will tell you Mody has been the driving force behind the development of Finn Delany, Will McDowell-White, Yanni Wetzell, Ousmane Dieng, Hugo Besson and RJ Hampton," Walsh said.
"His passion and excitement for the game are contagious. He has all the tools to be a great head coach and get us back to contending for championships."
Maor joined the club as an assistant in 2019. He has two years remaining on his current contract, and said it wanted to restore the pride Kiwi fans had in the club.
"We are coming off two difficult seasons in challenging circumstances, but what we really have now is a clean slate.
"There is a great kiwi core out there for us to recruit, and you can expect an exciting team pulling on the Breakers' jersey next season.
"We have an opportunity to rebuild, remake and reinvigorate."