The US rapper was condemned by Jewish groups after making comments criticising Israel.
Zendaya, Noah Wyle, Sarah Snook and Colman Domingo are among the stars nominated for acting prizes.
Backstage, the winners continued the celebrations off-screen and addressed some of the ceremony's most viral moments.
The 78th Primetime Emmy Awards were hosted by Law & Order star Mariska Hargitay at the Peacock Theatre in Los Angeles.
He becomes the first person to win two lead acting prizes in one night at the prestigious TV ceremony.
Stars from the latest hit TV shows turn out at the biggest night in the US TV calendar.
Beyoncé, Cher, Elton John and Miley Cyrus have all worn Mackie's glittery ensembles.
