Amina bint Abdulhalim Nassar was executed in the northern province of Jawf for "practising witchcraft and sorcery," the ministry said in a statement carried by SPA state news agency.
It is not clear how many women have been executed in the desert-kingdom, but another woman was beheaded in October for killing her husband by setting his house on fire.
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Amnesty International said beheading took to 73 the number of executions in Saudi Arabia this year.
The London-based human rights watchdog condemned Monday's execution as "truly appalling," and called on the conservative kingdom to urgently halt the practice.
"The charges of 'witchcraft and sorcery' are not defined as crimes in Saudi Arabia", said Philip Luther, Amnesty's interim director of the Middle East and North Africa.
"To use them to subject someone to the cruel and extreme penalty of execution is truly appalling," he added in a statement, which stressed the "urgent need" to stop executions.
Rape, murder, apostasy, armed robbery and drug trafficking are all punishable by death under Saudi Arabia's strict interpretation of Islamic sharia law.
Luther described as "deeply disturbing" the huge rise in the number of executions in Saudi Arabia.
Many of those executed have had no defence lawyer and are not informed about the legal proceedings against them, according to Amnesty.
"While we don't know the details of the acts which the authorities accused Amina of committing, the charge of sorcery has often been used in Saudi Arabia to punish people, generally after unfair trials, for exercising their right to freedom of speech or religion," Luther said.
Earlier this month, Amnesty accused the oil-rich kingdom of conducting a campaign of repression against protesters and reformists since the Arab Spring erupted 12 months ago.
The rights group said Saudi Arabia was one of a minority of states which voted against a UN General Assembly resolution last December calling for a worldwide moratorium on executions.
Amnesty says Saudi Arabia executed 27 convicts in 2010, compared to 67 executions announced the year before.
