Johnson, 41, spent the last 11 seasons as the Commodores' pitching coach, including the last three as an associate head coach/pitching coach. He earned National Pitching Coach of the Year honors in 2004 and National Assistant Coach of the Year honors in '10.
In 2011, Johnson guided Vanderbilt to the school's first College World Series appearance. Eight of the team's pitchers were selected in the First-Year Player Draft, including a pair of first-round or supplemental first-round pitchers in Sonny Gray and Grayson Garvin.
Johnson also helped develop David Price, who was picked first overall by the Rays in 2007.
Johnson began his coaching career at Eastern Illinois in 1994, a season after he was an All Mid-Continent Conference pitcher there. He was the pitching coach at Southern Illinois from '95-97, and also managed in summer ball. He coached at Stetson University ('98-2001) before joining Vanderbilt in '02.
"I saw him as a lab technician almost," Vanderbilt head baseball coach Tim Corbin told the Tennessean newspaper on Monday. "The guy immersed himself in pitching. He immersed himself in the development of the kids. It was on his mind 24 hours a day.
"The thing I like about him the most is there's no gray with D.J. It's black or white. And he's very loyal to the kids and loyal to the program. He stood for all the right things."
Johnson replaces Dennis Llewallyn, who had just completed his second year as the Cubs' Minor League pitching coordinator and sixth with the team.
Carrie Muskat is a reporter for MLB.com. She writes a blog, Muskat Ramblings, and you can follow her on Twitter @CarrieMuskat. This story was not subject to the approval of Major League Baseball or its clubs.