Upon Warren's resignation from Congress in 1940, Bonner was elected simultaneously to complete the unexpired term, and was elected to the 77th Congress for a full term. He served for twelve full terms, from November 5, 1940, until his death from cancer in Washington, D.C., on November 7, 1965. During the 79th Congress, he chaired the Committee on Election of President, Vice President, and Representatives in Congress, and in the 84th through 89th Congresses, he chaired the Committee on Merchant Marine and Fisheries.
Bonner died in office in 1965 in Washington, D.C.; he is buried in Washington, D.C.
Legacy
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.
Bonner was the namesake of the former Herbert C. Bonner Scout Reservation, commonly known as "Camp Bonner", located near Washington, North Carolina. This is now known as the East Carolina Scout Reservation composed of Camp Boddie and the Pamlico Seabase. The portion of the camp on the North side on the Pamlico River still bears the name Camp Bonner and is the regular site of the council camporee for the East Carolina Council of the Boy Scouts of America.