Nowak was banished from NASA after an episode in 2007 when she confronted a romantic rival at an Orlando airport.
Since her dismissal, the 20-year Navy veteran has been working at a naval air training station in Texas.
Now, she is getting an "other than honorable" discharge for poor conduct and what Navy officials call "a complete disregard for the well-being of a fellow service member."
Nowak was accused of confronting Colleen Shipman in the parking lot of the Orlando International Airport in February 2007 after driving from Houston.
Shipman, an Air Force captain, had begun dating Nowak's love interest, former space shuttle pilot Bill Oefelein.
Police say Nowak sprayed pepper spray into Shipman's car. Nowak's attorney says the pepper spray never reached Shipman.
Nowak was sentenced in 2009 to a year of probation in the altercation after pleading guilty to burglary charges.
The Associated Press contributed to this report.