Nutrient deficiency, herbicide injury, and fungal disease are the common cause of yellow spots in St. Augustine grass. Out of all the grass varieties, St. Augustine is particularly sensitive to weed killers.
To fix the yellow spots, the first thing that you should check is the soil pH level before applying lawn fertilizer. If the result is more than 7 you have to add more soil acidifier and if it is below 6.5, you have to lime your lawn to balance the soil pH.
You should also test a weed killer in a tiny spot on your lawn to see how the grass will react to it. Weed killer brands often fail to include the grass varieties that can get injured using their formula. So, better check the labels first or test them in a small patch to be sure.
Once the soil pH is at the right level, you may start fertilizing the soil with nitrogen fertilizers or add manure.