Atwal, the first Indian to win on the PGA Tour, had four bogeys in his first 11 holes, before two birdies on 15th and 16th saved him from total disaster.
It has been a disappointing year for Atwal, who has made just 13 cuts in 24 starts and is lying 171st on the Money List.
Nick O'hern shot a career-best 9-under 62 yesterday in rainy conditions to take a three-stroke lead over European Ryder Cup player Nicolas Colsaerts, Jhonattan Vegas and Derek Ernst.
O'Hern had eight birdies in an 11-hole stretch and had a bogey-free round to tie the course record at CordeValle Golf Club.
Colsaerts is trying to earn a PGA TOUR card while being a special temporary member. He needs to finish the equivalent of 125th on the money list to earn a full 2013 card.
The Belgian player has earned USD 652,886, enough now for the 120th spot.