South Australia's Hughes had reached 63 not out when he was felled by New South Wales paceman Sean Abbott.
The incident has cast a pall over the SCG, and there was genuine concern for Hughes' condition as ambulances rushed to the ground.
He was attempting to play a pull shot, and the ball hit him flush.
After the ball cannoned into his helmet, Hughes stood dazed before crashing face-first onto the pitch.
The NSW players and umpires called for help immediately, and the tea break was called 30 minutes early.
A medical cart transported Hughes from the field.
The left-hander is bidding for selection in Australia's first Test team which plays India in Brisbane next week.
He was considered a leading candidate to replace injured number four batsman Michael Clarke.