Programs are usually divisible. Systems are not. A program divided in half is about half as useful as it otherwise would have been. A system divided in half is fundamentally different, and far less useful than as a distinct whole. Programs operate within systems.
Systems are catalysts and enablers to programs.
Many policies are a mix of program and system. A program of road-building is initiated to institute a system of transportation. A program of school construction and management is instituted to provide a system of education. A system is less efficient at doing just one thing than a program . But it is more efficient at doing many things.