The 23-year-old was struck on the thumb in the 35th over of the first ODI against Bangladesh while fielding at point and immediately left the field.
He was unable to bat and New Zealand lost the match by 43 runs by the Duckworth-Lewis method.
Williamson's left thumb was dislocated and an X-ray confirmed a small fracture, New Zealand Cricket (NZC) said in a statement.
"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," team physiotherapist Paul Close said.
"Kane is about six weeks away from playing again at this stage."
Luke Ronchi will replace Williamson in the squad for the remainder of the Bangladesh tour, while a captain and replacement player for the Sri Lanka tour will be named later.
(Writing by Sudipto Ganguly; editing by Nick Mulvenney)
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