The two ships of Proactiva Open Arms were escorted to the port of the capital of the Balearic island of Majorca by a Spanish police ship at 7:15 am.
The woman who was rescued is a 40-year-old from Cameroon named Josepha. Proactiva said it transported her to Spain for her "protection" and to enable her to testify freely.
Italy had earlier offered to take in the woman but not the bodies.
Proactiva accuses Libyan coastguards of having saved the rest of the migrants on board the dinghy but not the two women and the child, whom they say refused to board the rescue vessel and go back to Libya.
The NGO alleges that as a result, the coastguards left them and deflated the dinghy. Rescuers let air out of migrants boats to stop them from being re-used and this boat had been slashed with a knife.
Libyan coastguards denied Proactiva's accusations and said they rescued 165 migrants from a boat in the same area on Monday night, without leaving anyone on board.
They also pointed out a lack of resources, particularly for night operations.
Proactiva will hold a press conference in Palma later Saturday with NBA star Marc Gasol, who took part in the rescue operation.