Earnhardt was involved in the 25-car crash at the end of last week's NASCAR race in Talladega, Ala., which is apparently where the injury occurred.
Hendrick Motorsports officials said Earnhardt was diagnosed Wednesday with a concussion. He will miss Saturday's race in Charlotte, N.C., and the Oct. 21 race in Kansas City, Kan.
Earnhardt said he was originally injured in a wreck in April in Kansas City, and after he had headaches this week, doctors ordered a series of tests that indicated a concussion.
"I knew that I sort of had regressed and had a bit of a setback," he said. "When you know how your body is and when you know something is not quite right, I knew as soon as it happened that I had reinjured myself, for a lack of a better way to describe it.
"(The Talladega wreck) was not even half of the impact that I had at Kansas but it was enough to cause me some concern."
Regan Smith will fill in for Earnhardt in the No. 88 Chevrolet for both races.
Earnhardt said in 2002 that he drove in several races after suffering a concussion. That admission led NASCAR to change its rules on drivers returning to racing after crashes.
Earnhardt is 11th in the current NASCAR Chase point standings, sitting 51 points behind leader Brad Keselowski.
There are six races left on the Sprint Cup 2012 schedule.