This is quite straightforward using the Cactvs Cheminformatics toolkit (visit www.xemistry.com/academic for free academic downloads), though it does involve not-quite-foolproof Internet-based compound name resolution:

a) Download the FDA NDC database zip file and expand. It contains a file 'product.txt' with the relevant data.

b) Use one of the toolkit interpreters to either run a simple Tcl script

table dictloop [table read product.txt] row {
    set ndc [dict get $row PRODUCTNDC]
    puts -nonewline "$ndc\t"
    set d [dict create]
    foreach s [split [dict get $row SUBSTANCENAME] \;] {
        set s [string trim $s]
        if {[info exists resolved($s)]} {
            dict append d $s $resolved($s)
        } elseif {[info exists unresolved($s)] || [catch {ens create $s} eh]} {
            puts stderr "failed to resolve substance name $s"
            set unresolved($s) 1        
        } else {
            if {[catch {ens get $eh E_CID} cid]} {
                puts stderr "no PubChem CID for substance $s"
                set unresolved($s) 1
            } else {
                dict append d $s $cid
                set resolved($s) $cid
            }
            ens delete $eh
        }
    }
    puts $d
}

c) or a Python3 script

t=Table.Read('product.txt')
t.iteratorstyle = 'dict';
resolved={}
unresolved={}
for row in t:
    ndc = row['PRODUCTNDC']   
    print(ndc,'\t',end='')
    d={}
    for s in [w.strip() for w in row['SUBSTANCENAME'].split(';')]:
        if s in resolved:
            d[s] = resolved[s]          
        elif s in unresolved:
            print('failed to resolve substance name',s,file=sys.stderr)
            unresolved[s] = True
        else:
            try:
                e=Ens(s)
                try:
                    d[s] = resolved[s] = e.E_CID
                except:   
                    print('no PubChem CID for',s,file=sys.stderr)
                    unresolved[s] = True
                finally:
                    e.delete()
            except:
                print('failed to resolve substance name',s,file=sys.stderr)
                unresolved[s] = True
    print(d)