In a large mixing bowl, whisk together the instant vanilla pudding mix and milk until well combined. Continue whisking for about 2 minutes until the mixture thickens.
Add ground nutmeg, ground cinnamon, and vanilla extract to the pudding mixture, stirring to incorporate all flavors evenly.
Gently fold in the whipped topping until the mixture is smooth and creamy, ensuring no lumps remain.
Dip each graham cracker sheet quickly into the eggnog, allowing excess to drip off.
In a 9x13 inch baking dish, create a layer of the dipped graham crackers at the bottom, covering the entire base.
Spread half of the pudding mixture over the layer of graham crackers.
Repeat the process: add another layer of eggnog-dipped graham crackers followed by the remaining pudding mixture.
Top with another layer of graham crackers to finish.
For the chocolate ganache, melt the chocolate chips and butter in a microwave-safe bowl. Heat in intervals of 30 seconds, stirring between each, until smooth.
Pour the melted chocolate ganache over the top layer of the graham crackers, spreading evenly.
Chill the cake in the refrigerator for at least 4 hours or overnight to allow it to set properly.
Before serving, garnish with a sprinkle of nutmeg on top for an added festive touch.