Atwal fired three birdies on the ninth, tenth and 18th holes which were negated by bogeys at the fifth, 11th and 15th holes here.
Woods, playing after a long gap, had an early birdie and then went 13 holes without his second birdie.
He had four bogeys and at 73 he is in danger of missing the cut. Valero Texas Open winner Brendan Steele shot four-under 67 at CordeValle and he was joined in the lead by Briny Baird, Garrett Willis and Matt Bettencourt.
PTI