Atwal's 67 saw him move to eight-under for three rounds but that was not enough as he exited from the Play-offs after finishing 109th on the FedEx standings.
Only the top 100 on the FedEx standings will move to the next tournament - the Deutsche Bank Championships.
The top 70 after the next leg will move to BMW Championship. In the last leg, the Tour Championships, only top 30 left at that stage will play for the FedEx Cup title.
Atwal is now likely to figure next in the Fall series, which begins after the four event FedEx Cup Playoffs.
With Hurricane Irene forcing the shortening of the event, Dustin Johnson turned in a brilliant six-under 65 in the third and final round to register a two-shot win over Matt Kuchar.
The title also helped Johnson move to the top of FedEx standings. Johnson shot 29 on the front nine at Plainfield Country Club for the second day in a row. Johnson finished at 19-under 194.
If the third round had not been completed, then Kuchar on the basis of his second round lead would have been declared the winner.
Though the rain came down when Johnson was on the fourth hole, it was not strong enough to force stoppage and he went on to finish and win his first title of the year and the fifth of his career.
Johnson, like Tiger Woods, has now won in each of his first four years since coming straight from college.
Atwal finishes 43rd, fails to make next stage of Play-offs
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