The girl had been born without a brain and Health Minister Maria Isabel Rodriguez says she died five hours after Monday's operation.
Officials refer to the 22-year-old mother only as Beatriz for privacy reasons.
The country's Supreme Court last week prohibited an abortion for Beatriz, who suffers from lupus and kidney failure.
Her lawyers said the pregnancy was threatening her life.
Her plight drew international attention and a ruling from the Inter-American Court on Human Rights that El Salvador should protect her life and help her to end the pregnancy.
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