Atwal, who shot a three-over 74 was inside the second round cutline of 148, following which 80 players qualified for the weekend.
But after the third he was tied for 74th and as per the 'MDF' ruling, he was left out of the final round yesterday.
He will, however get the money for tied 74th.
Atwal, starting on the tenth bogeyed 11th, 15th, third and eighth and had just one birdie on the sixth.
On a day that saw very few spectators, Brendon de Jonge shot 69 and moved into the lead by one shot. He led Tiger Woods (67), Bo Van Pelt (67) and No Seung Yul (69) and the trio was at six-under 207.
De Jonge was at seven-under 206 and will play in the final group with Van Pelt and Woods, who is going for his third win of the year.
Woods won the AT&T National the last time it was held at Congressional in 2009.