Clad in white robes denoting a state of purity and face masks, men and women cast their stones, closely monitored by health professionals.
The pilgrims stood apart on yellow markers marking a safe social distance.
The ritual, at which pilgrims must hurl pebbles at a giant wall, has in the past been the scene of several deadly crowd accidents.
In 2015, hundreds died in a crush at an intersection leading up to the site.In previous year, some 3 million white-clad pilgrims from across the world flocked to Islam's holiest sites to attend haj.
But with large gatherings impossible given the pandemic, only a few thousand pilgrims - Saudis and foreign residents living in the country- are gathering this year.
Although no official figure has been given, local media report there are around 10,000 pilgrims. The Haj minister in June said pilgrims would number 1,000.