This year, Saudi unveiled a fifth level of the bridge.
After the stoning, pilgrims cut or shave their hair, pay to have a livestock animal killed on their behalf to feed the poor, and head to Mecca.
Saudi TV footage showed thousands of pilgrims who had reached the Grand Mosque in Mecca by mid-morning to perform a ritual circulation of the Kaaba.
Despite a late downpour, the stoning was orderly, fulfilling Saudi hopes that enlarged pillars and the newly built walkway would end deadly stampedes as the faithful jammed into the area for the required ritual.
Pilgrim camps soaked
Thunderstorms earlier in the week had soaked the pilgrim camp sites in Mina and related floods have killed more than 80 people in the city of Jeddah so far.
Thousands of pilgrims were also reported to have been stuck in Jeddah because of the flooding, unable to begin Hajj.
A possible outbreak of H1N1 had been one of the biggest concern leading up to the start of Hajj, but Saudi authorities insist spread of the illness has been contained.
The last figures from the Saudi health ministry were 67 confirmed cases of H1N1 among pilgrims, with four of them in critical condition, and at least four deaths.
Elsewhere around the world, Muslims will be celebrating the holiday with a special morning prayer, passing out sweets and visiting family and friends.
Pilgrims will continue Hajj rites for the next two to three days, camping out at Mina and stoning the three columns representing the devil daily.
Hajj is one of the five pillars of Islam and it is mandatory for all able-bodied Muslims with the financial means to undertake it once in their lifetimes.