Syrian President Bashar al-Assad, his opposition, U.S.-backed Kurdish forces and the Islamic State militant group (ISIS) all recognized Eid al-Adha.
Mounting tensions between Qatar and its neighbors spilled over in June, when Saudi Arabia, Egypt, the United Arab Emirates and Bahrain all cut diplomatic ties with Qatar.
The Kaaba, meaning “cube” in Arabic, has been the center of Islam since the time of Prophet Muhammad, but it was worshipped for centuries prior.
Qatar has accused Saudi Arabia of deliberately making it difficult for its pilgrims to obtain permits to go to Mecca.
Seven of the Boeing 777s will fly Qatari pilgrims from Doha to Jeddah to attend the annual Hajj pilgrimage.
Almost 300 Nigerian pilgrims died in the 2015 stampede in Saudi Arabia.
Muslims from Sierra Leone were banned from going on Hajj during the Ebola outbreak.
Hundreds of Iranians died in a crush during last year's pilgrimage; both countries accuse each other of politicizing the hajj.
The Associated Press puts the dead at 1,399, while the official Saudi estimate is 769.
The Iranian president has warned "the Islamic Republic is prepared to use force."
More than 700 people died at an event during the Muslim hajj pilgrimage.