It's quite simple. The hard work is working out what the path to the USB device is. We need to start by finding which device we want to disable. We can do this with lsusb:

Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub

Bus 002 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub

Bus 001 Device 002: ID 0402:5602 ALi Corp. M5602 Video Camera Controller

Bus 001 Device 003: ID 045e:0723 Microsoft Corp. LifeCam VX-7000 (UVC-compliant)

Change 1-6 to your device ports to be disabled. The port often isn't logical (it's physical) but you can get a port mapping with lsusb -t. Once you think you have it, you can test it with:

cat /sys/bus/usb/devices/1-6/id{Vendor,Product} 

This gives me 0402 and 5602, vendor and product IDs for the right device (as listed in lsusb).

Now we've found it, turning it off is simple:

echo "0" > /sys/bus/usb/devices/1-6/bConfigurationValue

After making sure it works as desired, make it load every startup (for example, in /etc/rc.local.)