The disqualification for using a non-conforming driver was announced before Howell began the third round.
Howell shot 68 on Friday to move to 6-under, five strokes behind leader Patrick Reed.
PGA Tour rules official Tony Wallin said another official told him about Howell’s driver early Saturday morning.
He said the weight port cover came off Howell’s TaylorMade driver while he was on the driving range before his second round.
Had the cover come off during the round, Wallin said Howell would have been OK to play with it as long as he fixed it before his next round.