SEOUL—South Korean prosecutors indicted de facto Samsung leader Lee Jae-yong on charges of bribery and four other offenses, setting in motion legal proceedings that could put the tycoon behind bars for years.

The 48-year-old vice chairman of Samsung Electronics Co. was arrested Feb. 17 but prosecutors didn’t press formal charges until their Tuesday deadline. In addition to bribery, prosecutors accuse Mr. Lee of embezzlement, perjury, hiding assets abroad and concealing profit gained from criminal acts. Four other Samsung group...