Recently my motherboard's built-in USB ports started malfunctioning. On Windows it said power surge in USB port, and in Linux it says nothing but also in Linux USB ports malfunction. So I installed a PCI card that have USB port in it. And in Windows I can disable malfunctioning ports by device manager. How can I disable those malfunctioning USB ports.
Probably the easiest way is through the BIOS; many BIOSes have an option to disable onboard USB.
Disabling it in Linux would involve preventing the driver for the USB controller from loading. This wouldn't work if the chipset in your motherboard USB controller is the same as the chipset in your PCI USB controller.
Do some research on your motherboard and find out who makes the USB controller on it. You might be able to find out with a simple
I'm sure there's a way to identify by some sort of unique ID and then disable or "unregister" certain USB "branches" in the USB "tree"; hopefully a more enlightened person can share if possible.
You can switch off the power to a USB port with
I don't know if this has the same effect on the hardware as disabling the port through the BIOS or Windows.