The story
The phrase originates in the Old Testament, 2 Samuel 1:19. The earliest version in English is found in the Great Bible, (1539): Oh howe are the myghtie ouerthrowen. The modern word fallen version is found in the King James Version, (1611) and is an expression of David's lament over Saul and Jonathan: The beauty of Israel is slain upon thy high places: how are the mighty fallen!
Etymology from Wiktionary, CC BY-SA 4.0.