Goffin beat France's Gilles Simon 3-6 6-2 6-1.
Berdych was coming off a marathon win against Richard Gasquet on Tuesday and did not have enough left to challenge Djokovic. He won just six of his 23 second service points and was broken four times.
Djokovic improved to 26-1 this year. His only defeat came in February when he was forced to retire against Spain's Feliciano Lopez in Dubai due to an eye infection.
He has yet to drop a set in Miami, despite his issues with Austria's Dominic Thiem in the fourth round.
(Writing by Jahmal Corner in Los Angeles; Editing by Greg Stutchbury)
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