World’s No 1 tennis player was set to play third-seeded Simona Halep of Romania in the second semi-final.
Serena Williams, 33, was playing at Indian Wells for the first time in 14 years, having ended her boycott that began after she won the title in 2001 and was booed.
Simona Halep, 23, will face Jelena Jankovic in the final after the Serb fought back to beat Sabine Lisicki 3-6, 6-3, 6-1.
In a post on her official Instagram account, Serena Williams wrote: “Four months ago I began a journey to play Indian Wells and it was amazing.
“I never dreamed I could do it. But I would not have been able to do this without my fans.
“Though it ended early due to injury this year, I have to say I cannot wait to try again next year.”
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