Minter has agreed to return to Baltimore in the top job, having previously spent four years as an assistant coach with the Ravens under Harbaugh.
The 42-year-old then worked in the college game before returning to the NFL as the Los Angeles Chargers defensive co-ordinator for the past two seasons.
“This is an organisation whose values, culture and tradition of excellence reflect everything I believe about the game of football and how it should be played,” said Minter.
Ravens owner Steve Bisciotti added: “He clearly understands the values, high expectations and history of the Ravens, and he has a great vision for the future.”
Harbaugh had been in charge of the Ravens for 18 years so Minter will be just the fourth head coach in the team’s 31-year history.
He also had a second interview with the Las Vegas Raiders and cancelled an interview with the Cleveland Browns.