Maqbul bin Madi al-Sharari hit his son Mohammad “repeatedly with a cane on the back of his head and the rest of his body,” the ministry said in a statement carried by SPA state news agency.
He also punched the toddler in the face repeatedly and “burned him in different parts of his body, torturing him several times, which led to his death,” the ministry said.
Sharari’s execution in the northern Jawf region, brings to 18 the number of death sentences carried out this year in the ultra-conservative kingdom.
Saudi Arabia beheaded 78 people in 2013, according to an AFP count.
Last year, the U.N. High Commission for Human Rights denounced a “sharp increase in the use of capital punishment” there since 2011.
According to rights group Amnesty International, the number of executions rose from 27 in 2010, including five foreigners, to 82 in 2011, including 28 foreigners.
In 2012, the number of executions dipped slightly to 79, among them 27 foreigners.
Rape, murder, apostasy, armed robbery and drug trafficking are all punishable by death under Saudi Arabia’s strict version of Islamic sharia law.