Officials said they finished the investigation and calculated she is 13 years old, with a margin of error of about eight months.
Although authorities originally believed her 17-year-old boyfriend was the father of the baby, a DNA test determined the stepfather, 44, was responsible for the pregnancy.
Officials said he has been arrested and could face 12 to 20 years in prison.
ElUniversal.mx said the girl's mother did not find out she was pregnant until she was seven months along.
The girl and her daughter are now in a shelter provided by the government while the investigation concludes, ElUniversal.mx said.
The baby was born in Zoquipan, Mexico, Jan. 27, and officials said both the girl and her baby are healthy.