Ehud Netzer, 76, fell on Monday when a railing he was leaning on gave way at the Herodium archaeological site in the occupied West Bank where the grave of the first century BC king was found.
He was taken to hospital where he succumbed to his injuries late yesterday.
The Hebrew University professor discovered the tomb in 2007 after a three-decade search and has since excavated an elaborate mausoleum and three shattered sarcophagi believed to be those of Herod and two of his wives.
Herod is well-known among Israelis and Jews worldwide as the builder of the Second Jewish Temple in Jerusalem, of which only the outer wall, Judaism's most important pilgrimage site, remains.
The Gospel of Matthew describes how the Roman-era king ordered the murder of all boys in the Bethlehem area under the age of two in an attempt to prevent the infant Jesus from usurping his position as king of the Jews.
Most historians doubt the veracity of the story but believe that Herod was responsible for other acts of brutality, including the killing of at least one of his 10 wives and two of his children.
