Evelyn Hernández had always maintained she was innocent, saying that she did not know she was pregnant and lost consciousness during the birth.
Prosecutors had asked for a prison sentence of 40 years.
Her case has been closely watched in El Salvador and abroad with women's rights activists calling for her acquittal.
El Salvador has one of the strictest anti-abortion laws in the world. Abortion is illegal in all circumstances and those found guilty face between two and eight years in jail.
But in many cases, including the one against Ms Hernández, the charge is changed to one of aggravated homicide, which carries a minimum sentence of 30 years.
"Thank God, justice has been done," she said as she stood on the steps outside the court house, free after 33 "hard" months behind bars. "My future is to continue studying and to move forward with my goals. I am happy," she said.
"I am about to explode with happiness," her defence lawyer, Bertha Maria Deleon, tweeted.
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