Try completely cutting power to the system -- power down normally, then unplug the main power cord and wait a few minutes before plugging it back in and turning back on. I've seen motherboards which will disable USB ports if they detect a power overload, and won't reset it until the motherboard is hard power cycled.
Then test the ports with something else (mouse, thumbdrive, etc.)
If the ports are indeed dead, IMO it is unlikely (though possible) that the gamepad was responsible.
Nostalgia isn't what it used to be.