Chanting "Allah-o-Akbar" (God is the Greatest), pilgrims hurled seven pebbles each at the three walls representing the devil -- Jamarat Al-Sughra, Jamarat Al-Wusta, and Jamarat Al-Aqba.
After performing stoning, pilgrims turned towards Kaaba, raised their hands, praying for Allah's mercy and forgiveness.
Many pilgrims were seen crying with just a day to go for this year's Haj to end.
"Over 100 missing cases among Indian pilgrims have been reported which is comparatively less than last year," Indian Consul General B S Mubarak told PTI.
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"It was a once in a life-time experience. A feeling of fulfillment and satisfaction is there as we have completed an enriching and life-changing journey," V M Ibraheem, an Indian pilgrim from Kerala, told PTI.
Saudi King Abdullah in his address to Haj pilgrims called for concerted international efforts to fight and defeat the scourge which has nothing to do with Islam.
"Terrorism is neither attached to Islam nor to all other heavenly religions. It is a rotten element, which has no remedy to it except amputation," the King said in the address which was read out by Crown Prince Salman, deputy premier and minister of defence.
"With Allah's grace we are restlessly going to amputate it in order to protect our youth from engaging in extremist ideas and narrow self-interests, rather than decent Islamic brotherhood," he said.
Stoning at Jamarat is the main ritual pilgrims have to perform during the last three days of Haj, known also as Ayyam Al-Tashreeq.
Yesterday's stoning ritual was marred by by mild rain in the afternoon.
It is to emulate the stoning of Satan at three spots by Prophet Ibrahim where the devil is said to have appeared trying to dissuade him from obeying Allah's order to sacrifice his son, Ismail.