If you short circuit VCC and GND, then the supply voltage should be 0V.
--> There is no electrical energy available.
--> Impossible for anything to burn.
So either your description is wrong, or there is something else in your circuit providing energy to kill the micro.
--> please show the complete circuit, and provide a more detailed error description.
O.K. that makes more sense. Presumedly heavy overshoot during over current recovery.
A switching regulator with soft start after overcurrent shutdown would avoid the overshoot. It's difficult to provide an effective protection with TVS diodes, a 3.3V TVS diode has typical clamping voltage > 6V. If your regulator can't guarantee safe supply voltage, you may consider a SCR crowbar.
Very likely a recovery overshoot. Do you have access to a digital scope?
Solutions:
-Either a SCR crowbar as discussed previously, which would latch and you'll have to remove the main supply to unlatch it.
-Or replace the controller with one where a soft-start function could be implemented.