Before answering this question, let's first consider the meaning of the expression "somebody just walked over my grave." This saying is traditionally said after someone experiences random shivering; it is derived from folklore of the Middle Ages, when people believed the veil between the living and the dead was very thin.
In Aunt Alexandra's case, this expression seems to be an exclamation of prescience; without knowing it, she is anticipating that something awful will happen later that night. It is Halloween and in order to keep the children out of trouble, the ladies of Maycomb have organized a carnival at the school. Scout has been recruited to play a ham in the pageant organized by Mrs. Merriweather. Although an adult would normally escort the children when they leave the house after dark, Atticus "couldn't stand a pageant" after his Montgomery excursion and Aunt Alexandra is too tired after spending the afternoon decorating the stage.
Thus, the two children begin their "longest journey" when they walk home alone later that night and are violently attacked by Bob Ewell in the dark. Aunt Alexandra's comment seems to predict this near-death experience, and it also harkens to the theme of superstition that appears throughout the book, particularly around the approach of death.