Anthony Gann was lodged Thursday in the Lancaster County jail on suspicion of manslaughter.
Seward County Sheriff Michael Vance said Gann resigned from his position with the Sheriff's Office because of the indictment.
Gann turned himself in to authorities Thursday after the indictment was formalized. His bond was set at $100,000, meaning he would have to pay $10,000 to be released.
He is expected to make his first court appearance Monday.
The Nebraska State Patrol has not provided the Seward County Sheriff's Office with its investigation of the incident that occurred in October, Vance said.
An internal investigation by the Sheriff's Office did not find that Gann committed any violations or broke procedure during the shooting incident, Vance added.
The incident happened on Oct. 23 on I-80, beginning at about 3:10 p.m., when the deputy tried to stop a driver, later identified as 43-year-old Jorge Santana-Ramirez, in Seward County.
Santana-Ramirez turned around and drove the wrong way, going east in the westbound lanes, then crossing into the eastbound lanes before eventually stopping on the western edge of Lancaster County, according to a news release the Sheriff's Office issued the week of the shooting.
Gann had tried to stop the same vehicle the week prior in Seward County after seeing illegal substances in plain view, Vance said, but discontinued a pursuit in that instance.
When the deputy recognized the same car in Seward County the following week, he again attempted another traffic stop, pursuing the vehicle into Lancaster County, where the fatal shooting took place.
There were two deputies on scene once the car stopped after the chase. When they approached the driver, authorities said they noticed a weapon in the suspect's hand, which is what led to the shooting.
Officials did not say what the weapon was, and no further details about the shooting were provided in the days after the incident.
Deputies and Nebraska State Patrol troopers at the scene attempted life-saving measures, but Santana-Ramirez died at the scene.
As is the case whenever a person dies while in custody or while being apprehended by law enforcement in Nebraska, a grand jury was convened to determine if any laws were violated during the incident.
If 12 or more members of the 16-person grand jury determine that there is probable cause to believe a criminal offence has occurred, it results in a true bill being returned and the grand jury determines the violation to be included in the indictment.
The grand jury returned a true bill in the death of Santana-Ramirez on Thursday.
Lancaster County Attorney Pat Condon said in an email to the Journal Star that the grand jury documents will remain sealed until Monday.
Review of police shootings in Lincoln since 2013
1. Douglas DaMoude, May 30, 2014
2. Tyson Hubbard, March 5, 2015
3. Tareik Artis, Sept. 22, 2015
4. Zachary Grigsby, Nov. 29, 2015
5. Germichael Kennedy, June 26, 2016
6. Thomas Sailors, Jan. 5, 2018
7. Christopher Brennauer, Dec. 29, 2018
8. Joseph Francis Cimino, Oct. 8, 2019
9. Hailey Stainbrook and Christian Alexander, Feb. 20, 2021