Binan Issa Hilal was shot while resisting officers during the raid on Thursday in the northern Jawf region, official news agency SPA quoted a ministry spokesman as saying.
She died in hospital and the two suspects, Suweilem al-Ruwaili and Naem Al-Khalaf, were detained.
Ruwaili was wanted in connection with a number of alleged attacks, including August's bombing of a mosque used by soldiers that left 15 dead.
He was being sheltered by Khalaf who was in a relationship with Hilal, the ministry said.