The remains of Judge Mohammed al-Jirani were found on a farm in the town of Awamiya in the kingdom's Eastern Province, which has been a hotbed of protests among the Shiite minority for years.
The raid took place last Tuesday and subsequent DNA tests confirmed that a body recovered was that of Sheikh Jirani, a ministry spokesman told the official Saudi Press Agency.
The ministry named the slain suspect as Salman al-Faraj, adding that he was wanted on suspicion of terrorism offences.
Considered close to the authorities, the judge had been the target of several attacks before his abduction.
In 2011, his house and car were set on fire and members of his family barely escaped the flames. In 2012, his house was attacked again by armed men who failed to capture him.
Sheikh Jirani was critical of the protest movement among his fellow Shiites and accused leading clerics in the community of being too close to Iran and neighbouring Iraq.
The Shiite community makes up between 10 and 15 percent of Saudi Arabia's population of 32 million.
The latest wave of unrest erupted in the summer when authorities began tearing down the historic Musawara district of Awamiya.
Authorities said that the walled neighbourhood's labyrinth of alleyways had become a breeding ground for "terrorists".
The demolitions prompted armed clashes between militants and security forces.
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