In the rain-hit qualifiers, Atwal shot 69 in the first two rounds played on the same day. The US Open will be held at the Olympic Club from June 14 to 17.
Atwal, needing a birdie on the 18th to get into a play-off for the last berth, dropped a bogey and finished at tied 15th.
Tommy Biershink (67-66) topped the qualifiers and other prominent qualifiers included Joe Ogilvie, Stephen Amex and Hunter Haas.
Roberto Castro, who had food poisoning the day before the event, got the last berth. Amateur Hunter Hamrick will make his professional debut at the US Open after finishing at eight-under 134.
None of the four major champions in the field -