Bradley's withdrawal could cost him a place in next week's elite Tour Championship in Atlanta, the last of the PGA Tour's four lucrative FedExCup events.
"I just feel withdrawing is the right thing to do to protect the field in the BMW Championship and the Tour Championship next week," Bradley said in a statement released by his management company.
Bradley's decision to pull out followed the withdrawal earlier in the day by compatriot Phil Mickelson, who had languished 14 strokes off the pace after 36 holes and said he wanted to rest for this month's Ryder Cup.
Bradley had been 11 strokes off the pace after the second round at Cherry Hills Country Club, having opened with scores of one-over-par 71 and 72.
However, he had lingering doubts over a drop taken in Thursday's first round after his third shot at the par-four 18th had embedded in grass just above a bunker.
After taking relief under Rule 25-2 for a ball embedded in its own pitch mark, he chipped on to the green and two-putted for a double-bogey six.
A spectator later told Bradley that he seen the ball bounce before it came to a rest in the grass face above the greenside bunker at the 18th.
Though a PGA Tour rules official subsequently absolved Bradley of any potential violation, the American decided to withdrew from the event due to his own uneasiness over the incident.
"It's eating me alive," said Bradley, a three-times winner on the PGA Tour who clinched his first major title at the 2011 PGA Championship.
"I didn't call my fellow competitors for help in the first place and that bothers me. I know the official approved the drop but I just can't be absolutely sure it was the right spot."
The leading 30 players on the FedExCup points list after the BMW Championship advance to next week's playoff finale in Atlanta. Bradley was 28th in the standings coming into this week, but is now projected to fall out of the top 30.
(Reporting by Mark Lamport-Stokes in Los Angeles; Editing by Gene Cherry)
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