Mohammed Murthi al-Zahrani "arrived here this morning" and security officials made preparations for him to meet his family, the ministry's spokesman said in comments carried by the official Saudi Press Agency.
Zahrani's departure leaves 142 prisoners at the jail US President Barack Obama has pledged to close.
Regarded as a previously active member of Al-Qaeda, Zahrani is the latest of seven prisoners freed from the controversial jail in Cuba in the past three weeks.
His release comes just days after authorities transferred five inmates to Georgia and Slovakia.
He was flown from the prison on a specially chartered flight on Friday.
Zahrani was once considered to present a "high risk" to American interests.
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He was approved for removal last month by a special review board created by Obama in his efforts to shut the prison, a Pentagon statement said, adding that Congress was duly informed of the transfer.
As part of the release deal Zahrani, 45, will take part in a rehabilitation and counselling program in Saudi Arabia.
The review board was composed of representatives from six government agencies including the State and Defence departments. It decided on October 3 that Zahrani no longer represented a threat to the United States.
Ian Moss, spokesman for Cliff Sloan, the State Department envoy who negotiates transfer deals, praised the Saudi rulers and the "close partnership" between Washington and Riyadh.
Prisoners from many countries are still held in Guantanamo but the largest group is Yemeni.
One of the best known inmates is Saudi detainee Abd al-Rahim al-Nashiri, who is accused of masterminding a suicide bombing of the USS Cole which killed 17 American sailors in 2000 off the coast of Yemen.
He also faces charges stemming from a 2002 attack on the MV Limburg French oil tanker that killed a Bulgarian sailor.