The 21-year-old recently suffered a stress reaction in her foot and has been advised not to take part in Glasgow.
However, Johnson-Thompson is expected to be back in action next month.
"I'm absolutely devastated that I'm not going to be able to compete at the upcoming Commonwealth Games in Glasgow," she said in an official statement. "I was so looking forward to competing in another home games and this time as one of the favourites.
"The Commonwealths was a key target for me this year and I was feeling so good in my preparation up until this week so this is a real blow.
"All the advice is telling me that I risk long term damage if I compete in a heptathlon in just over a week's time and I have to take that advice for the sake of my career."