Atwal, India's first and only winner on PGA Tour, came through the Monday qualification to make the tournament, but could not progress to the weekend rounds.
It was only his second appearance on the PGA Tour this season. He missed the cut in first event also.
Chez Reavie shot a five-under 65 to move to nine-under 131 and share the lead with Charl Schwartzel and Sebastian Munoz after two rounds.
Ben Crane, who won this tournament in 2014, was two strokes off the lead after shooting a 65 at the par-70 TPC Southwind course.