"This is a great opportunity for John to further his career," USC coach Lane Kiffin said. "We appreciate the great work he did at USC and wish him the best of luck."
Morton joined USC in 2007 and spent three years as wide receivers coach under Pete Carroll. He was the only assistant retained by Kiffin, continuing in the same capacity last season.
In 2010, true freshman Robert Woods was named Pac-10 Freshman of the Year and honored on numerous Freshman All-America teams after catching 65 passes for 792 yards and six touchdowns under Morton.
Morton also helped Damian Williams develop into a first-team All-Pac-10 selection in 2009.
Morton and Harbaugh previously worked together in 2005 at the University of San Diego. Morton served as passing game coordinator under Harbaugh for one season before moving on to the New Orleans Saints.
Harbaugh signed a five-year contract with the 49ers earlier this month after guiding Stanford to its best season in school history, a 12-1 campaign capped by an Orange Bowl victory over Virginia Tech.
Harbaugh previously hired three Cardinal assistants, defensive coordinator Vic Fangio, associate head coach Greg Roman and offensive line coach Tim Drenvo, to join his staff.
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