The two-time U.S. Open winner had dropped three strokes in his first four holes in the second round, but parred his next six holes before pulling out.
Goosen, who shot a 75 in round one, bogeyed the first and second. After a birdie on the par-four third, the South African stumbled to a double-bogey on the par-three fourth.
He had dropped to plus-eight for the championship. Goosen, who shared sixth at the 2005 PGA Championship, also withdrew from the British Open.