Shafer replaces Doug Marrone, who left Syracuse to become the head coach of the NFL's Buffalo Bills.
"We will go to work every day to put a quality product on the field as we storm our way into the Atlantic Coast Conference," Shafer said. "We are very motivated to start preparing for the 2013 campaign with our current team and incoming student-athletes."
Shafer, 46, has never before been a head coach but has worked with programs at Michigan, Stanford, Western Michigan, Illinois, Northern Illinois and Rhode Island before joining the Syracuse staff in 2009 as Marrone's defensive coordinator.
The Orange defensive unit became one of the highest-ranked teams in the nation with Shafer as defensive coordinator.
Syracuse, which is leaving the Big East Conference for the ACC, won a total of 10 games in the four seasons before Marrone took over and was 25-25 with two bowl appearances since then.