Raisi, 63, was widely seen as a candidate to succeed 85-year-old Supreme Leader Ali Khamenei, who wields ultimate power in Iran.
Mohammad Mokhber, who had been first vice president, is serving as interim president until a June election.
The burial ceremony was attended by Iranian government and military officials, as well as religious personalities.
Flowers were thrown at his coffin as it moved slowly aboard a truck through throngs of mourners to be buried at the gold-domed Imam Reza shrine, Iran's holiest Islamic site and revered as the resting place of the 9th century Imam Ali al-Reza.
President Ebrahim Raisi and Foreign Minister Hossein Amirabdollahian died in a helicopter crash. (AP PHOTO)
Raisi hailed from Mashhad, 900km east of Tehran.
Earlier, thousands had paid their respects as his coffin was driven in a motorcade through the eastern city of Birjand.
Eight passengers and crew were killed when the helicopter crashed in mountainous terrain near the Azerbaijan border.
They included Foreign Minister Hossein Amirabdollahian.
Iran proclaimed five days of mourning for Raisi, who enacted the hardline policies of his mentor Khamenei aimed at entrenching Shi'ite clerical power, cracking down on public dissent and adopting a tough line on foreign policy issues such as talks with the US to revive Iran's 2015 nuclear pact.
The presidential election has been scheduled for June 28.
A ceremony was held to commemorate Amirabdollahian at the foreign ministry in Tehran, where acting Foreign Minister Ali Bagheri Kani described him as a martyr who had "guaranteed the revolutionary nature of the foreign ministry".
Amirabdollahian was buried south of Tehran in the city of Rey's Shah Abdolazim shrine, a mausoleum where notable Iranian politicians and artists are interred.
