The 24-year-old top-edged a bouncer from Irfan Pathan and the ball struck him above the right eye, wedging between the visor and peak of his helmet.
Vermeulen, who suffered a hairline skull fracture during a net session at last year's World Cup, was taken to a Brisbane hospital where a depressed skull fracture was diagnosed. He is expected to have reconstructive surgery in Brisbane this week and will play no further part in the series.