The Ducati rider was flung up on top of his machine as he wrestled to control a high-side towards the end of his quick lap, smashing the screen with his helmet before being thrown off the bike and ending up lying unconscious by the side of the track.
Doctors quickly ruled the 2006 world champion out of the race at the Brickyard, but he had remained hopeful of being fit to compete at Brno.
But with his injuries still causing him discomfort, the American has elected to skip this weekend's race and return for the San Marino Grand Prix at Misano next month.
He said: "It's tough to miss another race. I don't have big problems, but my hand is still very swollen and I don't have much strength, and of course right-hand injuries are worse for motorcycle racers.
"I would have been at far less than 100% and if I used too much force or crashed again, I could displace the breaks and possibly be in big trouble.
"Obviously, the head is even more important and with the amount of time I was unconscious, I'm still dealing with a headache.
"The main thing is all the doctors told me racing was a really bad idea and not smart, and everybody on my team agreed.
"As much as the racer in me doesn't like staying at home and missing track time and points, I need to listen to the experts and try to heal up and get ready for Misano."