The 25-year-old finished fourth in the 800 metres to wrap up the crown and add it to her World Indoor pentathlon title.
Favourite Johnson-Thompson was nowhere near her best but still comfortably finished 122 points ahead of Canada's Nina Schultz.
England's Niamh Emerson won bronze after claiming victory in the 800m.
25-year-old Johnson-Thompson appeared to be struggling through the 800 metres and confirmed she was battling a calf injury.
"I was nursing an injury going into day two," she said. "It got worse about 300 metres into the (800 metres) race. I'm just happy I made it over the line, there was no way I was stopping. I'm so happy. It's been a long emotional two days but i'm glad it's finally over.
"Considering it's only April, I'm really happy to get season best performances this early and come away with the gold.
"I feel like this Championship was mine, I was devastated to pull out four years ago in Glasgow but I've got two gold medals now and it's more than I could ask for this early in the season."
Johnson-Thompson knows she will face much tougher opposition in the European Championships in Glasgow in August but nevertheless savoured her Commonwealth title.
"I know I have not set the world alight with some of my events but coming here not knowing what to expect I'm so happy to come away with the gold.
"I really wanted this under my belt and I think it's going to give me a lot of confidence going forwards.
"I've now got 16 weeks to get myself ready for the Euros."
Register for free to continue reading
Registration is a free and easy way to support our truly independent journalism
By registering, you will also enjoy limited access to Premium articles, exclusive newsletters, commenting, and virtual events with our leading journalists
Already have an account? sign in
Join our new commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies