Health authorities said no coronavirus cases were reported at the holy sites during the hajj, one of the five pillars of Islam and a must for able-bodied Muslims at least once in their lifetime.
Hajj pilgrims circled the sacred Kaaba — a cubic structure inside Mecca's Grand Mosque towards which Muslims around the world pray — along socially distant paths.
The pilgrims were also subjected to regular temperature checks and required to go into mandatory quarantine after the ritual.
King Salman, the kingdom's 84-year-old ruler, said holding the hajj in the shadow of the pandemic required "double efforts" by Saudi authorities.
The hajj and umrah pilgrimages are a massive logistical challenge, with colossal crowds cramming into relatively small holy sites, making them vulnerable to contagion.
The kingdom has sought to contain a spike in infections, which have now risen to more than 330,000 cases — the highest in the Gulf — and over 4,500 deaths.
But Saudi Arabia has also reported a high rate of recoveries, which surpassed 312,000 on Tuesday.
Last week, Saudi Arabia partially lifted its suspension on international flights, six months after travel curbs were imposed due to the pandemic.