 Bonner died in office in 1965 in Washington, D.C.; he is buried in Washington, N.C. 

A former bridge spanning Oregon Inlet on the Outer Banks was named in honor of him and his service to the state of North Carolina.When the bridge was replaced in 2019, 1,000 ft of the Bonner bridge was left to be used a pier and retains the Bonner name.The M/V Herbert C. Bonner, a 25 car ferry was also named for him.