"The two girls are now in safe hands with the Saudi authorities," said Westerwelle.
"Considering the circumstances they are doing well."
Mansour al-Turki, a Saudi Arabian interior ministry spokesman, gave few details on the operation or on the fate of the other family members.
Westerwelle said he remained concerned about the three other German citizens who were abducted.
In December, Yemen's deputy defence minister accused al-Qaeda of the kidnapping.
Separately, Yemeni and Chinese officials said kidnappers released two Chinese oil workers on Tuesday after they were abducted in Yemen on Sunday.
"The two Chinese hostages were liberated after tribal mediation and government pressure," a tribal source in Yemen said.
Yemen's interior ministry confirmed the release of the Chinese pair, saying they "are in good health."
The two were seized along with two Yemeni drivers and two soldiers.
All six have been released, according to the local official, who confirmed that the "men are now with representatives of the local authorities in Shabwa province," 750km from Sanaa.
Yemen's powerful tribes frequently carry out abductions of foreigners to try to secure bargaining counters in disputes with the central government.
Of the 200 or so foreigners seized in Yemen over the past decade, most have been released unharmed.