The authority over U.S. coinage is established in the Constitution (Article I, Section 8), which gives Congress the power "to coin Money, regulate the Value thereof." Any major changes to U.S. currency, including eliminating a denomination, must go through Congress.
>“The Secretary of the Treasury shall,” Section 5111 reads, “mint and issue” denominations of coins “in amounts the Secretary decides are necessary to meet the needs of the United States.”