Saban led all coaches in salary in USA Today's survey last year, at $7,087,481.
Harbaugh's $9,004,000 salary includes two $2 million interest-free loans -- coming in the form of annual life-insurance premium payments -- one of which he received June 3 and the other he will receive if he is still coaching Michigan on Dec. 6.
Rounding out the top five are Ohio State's Urban Meyer at $6 million, Oklahoma's Bob Stoops at $5.5 million and Florida State's Jimbo Fisher at $5.25 million.
Texas' Charlie Strong is next at $5.2 million, followed by three SEC coaches -- Texas A&M's Kevin Sumlin at $5 million, Auburn's Gus Malzahn at $4.725 million and Mississippi's Hugh Freeze at $4.7 million.
The SEC had the highest median coach salary at$4,172,500, followed by the Big 12 ($3,540,788), the Pac-12 ($3,102,960), the Big Ten ($2,753,100) and the ACC ($2,562,485).
Penn State's James Franklin rounds out the top 10 at $4.5 million.
Dabo Swinney, coach of No. 3 Clemson, is No. 12 at $4.4 million. Washington's Chris Peterson, coach of No. 4 Washington, is No. 25 at $3.6 million. Nebraska's Mike Riley, whose Cornhuskers are ranked No. 7, is No. 42 at $2.8 million. Dana Holgorsen, coach of No. 10 West Virginia, is 37th at $2.98 million.
Among other notable names, Notre Dame's Brian Kelly is far down the list, 65th among coaches ranked, at a salary of $1.625 million.
Thirty-six FBS coaches are earning at least $3 million this year, up from just nine in 2011.
USA Today reports that at least seven FBS coaches -- not all contracts are public -- would be owed at least $20 million guaranteed if they were fired after the regular season. Fisher would have the highest buyout at $33 million, and Iowa's Kirk Ferentz would be owed more than $25 million.
Of the 53 publicly available contracts for Power 5 coaches, 33 include buyouts of at least $8 million.
ESPN's Adam Rittenberg contributed to this report.