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It does look like in additional to the South African LH/SA codeshare, Lufthansa operates flights between FRA and CPT/JNB with their own aircraft.

Their current schedule:

Sun/Wed/Fri
FRA-CPT nonstop
LH 2954 (operated by South African Airways) 1910/0705 (+1)

Sat only
FRA-CPT nonstop
LH 576 (operated by Lufthansa) 2225/1015 (+1)

Mon through Fri
FRA-CPT via JNB
LH 572 (operated by Lufthansa) 2240/1210 (+1)

Mon through Sat
FRA-JNB
LH 572 (operated by Lufthansa) 2240/0850 (+1)

Mon through Sat
FRA-JNB
LH 2940 (operated by South African Airways) 2045/0725 (+1)