Parade Chairwoman Madelyn Lugo on Sunday said the parade is about "pride and respect" and that Captain Morgan has shown neither.
Diageo's other brands include Johnnie Walker and Jose Cuervo.
The liquor company has a deal to build a Captain Morgan distillery in the U.S. Virgin Islands for a share in the territory's portion of an obscure tax on U.S. rum sales.
Diageo didn't immediately respond to an e-mailed request for comment about the parade's decision.
This year's parade is scheduled for June 13.