Atwal, who was lying way down after a two-over 73 in the first round, ended at even par 142 while the cut came at one-under 141.
The Indian started at the tenth and bogeyed the 13th, but then birdied the 15th, first and sixth.
John Mallinger opened a four-stroke lead following an eagle and two birdies on the final four holes for a course record-tying 9-under 62. He eagled the par-5 15th and closed with consecutive birdies to reach 14 under.
The 33-year-old Mallinger is winless in seven seasons on the PGA TOUR.
Billy Horschel (65) and Jhonattan Vegas (67) were second at 10-under 132. Nicolas Colsaerts (68), Nick O'Hern (71) and Scott Dunlap (63) were tied 4th at nine-under 133.