Williamson was struck on the thumb in the 35th over fielding at point, and immediately left the field. His left thumb was dislocated and after specialist treatment at a local hospital, an X ray confirmed the small fracture.
"This kind of injury unfortunately means Kane cannot take part in the rest of the tour and he'll return to New Zealand to begin his rehabilitation - Kane is about six weeks away from playing again at this stage," said New Zealand physiotherapist Paul Close.
Luke Ronchi will travel to Bangladesh to replace Williamson in the touring squad. The captain for the Sri Lankan ODIs and an additional player to join the squad for that leg of the tour will be named at a later date.