Williamson suffered the injury in Bangladesh earlier this week and had already returned home for treatment, New Zealand Cricket (NZC) said.
He had been expected to lead the side for their three one-day internationals and two Twenty20 matches in Sri Lanka after NZC decided captain Brendon McCullum and his predecessor Ross Taylor would return home after the Bangladesh tour to prepare for series against West Indies and India.
Rob Nicol will replace Williamson in the squad, while all rounder Andrew Ellis has been called up due to a back injury to Otago bowler Ian Butler.
"It's disappointing that Ian's back didn't settle in time for the Sri Lanka tour," national selection general manager Bruce Edgar said. "We'll also bring in Otago's Neil Broom for the final ODI and the two Twenty20s as additional cover."
Tim Southee, who had ankle surgery in July, is also returning after the Bangladesh tour so he can prepare for the West Indies series, which starts with the first test in Dunedin on December 3.
New Zealand's tour of Sri Lanka begins on November 10 with the first one-day international in Hambantota and concludes on November 21 after the second Twenty20 international in Kandy.
Revised New Zealand squad: Kyle Mills (captain), Corey Anderson, Neil Broom, Anton Devcich, Grant Elliott, Andrew Ellis, Tom Latham, Mitchell McClenaghan, Nathan McCullum, Adam Milne, Colin Munro, James Neesham, Rob Nicol, Luke Ronchi, Hamish Rutherford
(Reporting by Greg Stutchbury; Editing by Peter Rutherford)
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