Mecca's provincial governor, Prince Khaled al-Faisal bin Abdul Aziz, said the 2013 Haj marked a "qualitative turning point" in the organisation of the annual pilgrimage, marred in previous years by deadly fires and stampedes.
The rites were carried out in a calm atmosphere and free of any political demonstrations, making it a "success" and proving "Islam is a religion of peace, civilisation and progress," he told reporters.
Although the Haj, one of the five pillars of Islam, comes to a close officially on Friday, pilgrims are allowed to leave a day early after taking part in the stoning of the devil ritual.
The ritual is an emulation of the Prophet Abraham's stoning of the devil at the three spots where it is said Satan tried to dissuade the biblical patriarch from obeying God's order to sacrifice his son, Ishmael.
In 2006, more than 300 pilgrims were killed in a stampede during the stoning ritual, the most dangerous of the Haj. More than 250 were killed in a similar incident in 2004.
The deaths prompted the Saudi authorities to invest billions of dollars in transport and other infrastructure to facilitate the movement of the huge numbers of people who take part.
Muslims believe the Kaaba -- which they call the "House of God" -- was built by Abraham 4,000 years ago.
Thousands of pilgrims were later seen loading trucks with luggage and leaving their hotels in Mecca.
The majority of them make the 100-kilometre journey to Jeddah international airport to take flights back home.
Oil-rich Saudi Arabia deployed more than 100,000 troops to maintain the security of the pilgrims during the Haj.
There had been particular concern about the possible spread of the MERS virus, which has killed 60 people worldwide, 51 of them in the kingdom itself.
"Not a single case (of MERS) was detected," Health Minister Abdallah al-Rabia told reporters.
The overall number of pilgrims at this year's Haj was just under two million, sharply down on last year's 3.2 million. Foreign pilgrims accounted for 1.38 million of them, compared with 1.75 million in 2012. Officials said the smaller number contributed to the success.
