Tehran had accused Saudi Arabia of kidnapping Ghazanfar Roknabadi because he previously held sensitive positions for the Iranian government, such as the post of ambassador to Lebanon.
The daily IRAN newspaper reported today that officials identified Roknabadi through fingerprints and a DNA test.
Iranian state television said his body was exhumed in Mecca and would arrive in Iran on Saturday.
Iran, which lost 465 pilgrims in the Sept. 24 stampede in Mina, repeatedly has blamed the Saudi government for the disaster, accusing it of mismanagement.