According to Apple Computers and Displays: Powering peripherals through USB the only way to turn off power to the USB ports is to turn off the Mac, power will remain while the Mac is sleeping.
If your Apple computer or display is powered off, no power will be provided.
A work around for this is changing what your Mac Does when you close the lid. You can reconfigure your MacBook to go into a different safe sleep mode when you close the lid, as opposed to normal sleep. This is very similar to the hibernate feature available for Windows PC and would result in USB power being off.
The only con is that you would have to press the power button to start your mac when you open it. And it would take more time to get the Mac back to where you left off at, as it reloads the contents of RAM from disk.
You can change your Macs sleep-mode as indicated in Set newer portable Macs' sleep mode provided by MacWorld.
Check the current setup
$ pmset -g | grep hibernatemode
which mode is which:
0 - Old style sleep mode, with RAM powered on while sleeping, safe sleep disabled, and super-fast wake.
1 - Hibernation mode, with RAM contents written to disk, system totally shut down while “sleeping,” and slower wake up, due to reading the contents of RAM off the hard drive.
3 - The default mode on machines introduced since about fall 2005. RAM is powered on while sleeping, but RAM contents are also written to disk before sleeping. In the event of total power loss, the system enters hibernation mode automatically.
5 - This is the same as mode 1, but it’s for those using secure virtual memory (in System Preferences -> Security).
7 - This is the same as mode 3, but it’s for those using secure virtual memory.
It appears that sleep mode 1 would enable your USB ports to be powered off when closing the lid of the MacBook.
Change the sleep mode setting
sudo pmset -a hibernatemode 1