"It's a victory for the people of Bahrain," Sayed Al-Wadaei, director of advocacy at the Bahrain Institute for Rights and Democracy campaign group, told AFP after the hearing.
"The day of accountability has come for Bahrain," he said.
A lawyer for the anonymous survivor, Sue Willman, said she expected a meeting with the police's war crimes unit "in the next few weeks" to discuss taking the investigation further.
The survivor was referred to in court only as "FF".
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The decision has no immediate effect on the prince, who is not being prosecuted and considers Britain a home-from-home.
It could, however, lead to his arrest if the case is pursued.
Willman said the prince travels to Britain "frequently", particularly to attend equestrian events.
Al-Wadaei said the prince considers Britain "a second home".
Willman also said that while the decision applies only to Britain, it would be "influential" for other EU states.
It goes against a 2012 decision by British prosecutors that Prince Al-Khalifa would be entitled to immunity from arrest.
Tiny but strategically-placed Bahrain, home to the US Navy's Fifth Fleet, remains deeply divided three years later.
It continues to witness sporadic protests which often spiral into clashes with police.