Shayanna Jenkins was released on personal recognizance during her arraignment in Fall River Superior Court on a single perjury count. Prosecutors had sought $5,000 cash bail.
In August, Jenkins lied to the grand jury hearing evidence in the case, including about where she threw out a box Hernandez asked her to "get rid of" in the aftermath of Odin Lloyd's killing, Bristol County Assistant District Attorney Patrick Bomberg said.
Jenkins initially invoked her Fifth Amendment right against self-incrimination, but was later granted immunity for her testimony, Bomberg said.
Hernandez, 23, has pleaded not guilty to the June murder of Lloyd, a 27-year-old semi-pro football player from Boston who was dating Jenkins' sister. He is being held without bail.
In court Tuesday, Bomberg said that the day after Lloyd was killed, Jenkins retrieved the box from the basement of the home she shared with Hernandez in North Attleborough, Mass., put it in a trash bag, covered it with baby clothes and drove away with it. Jenkins repeatedly told grand jurors she threw the box in a Dumpster but couldn't recall where, according to Bomberg.
Bomberg did not say what is believed to have been in the box. Hernandez associate Carlos Ortiz, who is charged as an accessory in the case, has told investigators that Hernandez put firearms in a box in his basement after the killing, according to court records. Prosecutors have said the murder weapon has not been found.
Defence attorney Janice Bassil said Jenkins answered every question asked of her before the grand jury and that prosecutors were overreaching with the perjury charge. She said there is no evidence Jenkins lied and that prosecutors sought the indictment simply because they didn't believe her. She called lead prosecutor William McCauley's questioning of Jenkins "extremely aggressive" and heavy-handed.
Bassil described the relationship between Jenkins and Hernandez, who have a young child together, as one of "don't ask, don't tell." Bassil had no further comment outside court.
The perjury charge carries a maximum penalty of 20 years.
Prosecutors have asked the judge assigned to the Hernandez case, Susan Garsh, to recuse herself, saying she and the McCauley have a "well-known and publicly documented history of antagonism" stemming from a 2010 murder trial he argued before her.
McCauley won a conviction in that case but was quoted in the press as criticizing Garsh, saying she had unfairly limited or excluded evidence and exhibited antagonism. A hearing on the request is scheduled for Monday.
Three others face charges in the case. Ernest Wallace and Ortiz, who prosecutors say were with Hernandez and Lloyd in a car on the night Lloyd was killed, have been charged with being an accessory to murder after the fact.
Wallace has pleaded not guilty and is being held on $500,000 bail. Ortiz is scheduled to be arraigned Friday.
Hernandez's cousin, Tanya Singleton, has pleaded not guilty to charges of conspiracy to commit accessory after the fact and criminal contempt. Prosecutors say she refused to testify before the grand jury even though she was offered immunity.
Hernandez has also been linked to an investigation into a 2012 double homicide in Boston. While investigating Lloyd's death, police found a sport utility vehicle rented in Hernandez's name at the home of Hernandez's uncle in Bristol, Conn., that was wanted in connection with those killings.