Johnson was hired to replace Larry Fedora, who left Southern Mississippi to become the football coach at North Carolina. The Golden Eagles were 12-2 and ranked 19th in the final coaches' poll after last season.
But Southern Mississippi went 0-12 in 2012. It was the Golden Eagles' first losing season since 1993 and first without a win since they went 0-6 in 1925.
"Following a thorough assessment of our football program, I made the recommendation to our university president that we not retain Ellis Johnson as our head football coach," Southern Mississippi Athletic Director Hammond said in a statement Tuesday.
"At Southern Miss, we expect to compete hard and succeed both in the classroom and on the field. This is not the exception. This is in fact the standard, the norm, our identity and who we are."
Johnson previously coached at Gardner-Webb for one season and the Citadel for three. Counting Southern Mississippi, his overall coaching record is 17-40.