Atwal shot a round of five-over 75 for a total of six-over 286.
Atwal had just two birdies against five bogeys and one double bogey in his round yesterday.
Rookie Ted Potter Jr first got into a play-off with a six-under 64 and then beat Troy Kelly (66) in a play-off going into three holes.
It was Potter's first win and will give him a ticket to 2013 Masters. Charlie Wi (65) was third and Charlie Beljan (67) was tied with him.
Potter, who was second on the web.Com Tour last, previously known as Nationwide, also gets a two-year exemption, besides he and Kelly also got an entry in the British Open.