Saleh was most recently the linebackers coach of the Jacksonville Jaguars, but was part of the coaching staff overhaul there.
"Robert Saleh is as smart as anyone I've been around," Shanahan said. "He studies everything. He knows a lot of different systems, but he knows the true Seattle-Atlanta-Jacksonville system inside and out, as much as anybody I've been with."
Together, they'll try to overhaul a 49ers defense that ranked dead last in 2016.