Q: El Capitan shutting off USB power on MacBook Pro?

Max OS X 10.11.1 did NOT resolve 100% for me. Better but far from even 50% improvement on WHAT IT USED TO BE.

iPhone charges OK and overnight with lit close, but slow, terribly slow... iPad does not charge and shows bizarre behavior while plugged in after a while.

Some times my trackpad and keyboard stops for a while and return back. Extremely annoying, and some web plugins that needs to use the USB port (like Sony's PlayMemoriesApp webapp) are not working for me like it used to be neither on Safari nor Firefox.

What a joke. What a sad joke.

I'm having the same issue with my Mac Pro 2013 with my USB 3.0 hard drives not showing up on my desktop unless they are plugged into a powered hub.

Same here, very inconsistent behavior. Until I found this thread, I was convinced it was a hardware issue, and even had the motherboard replaced. For me the issues are extremely bizarre, but it all makes sense in the context of the OS (over)controlling power to the USB ports. I have a MBP Retina, 13-inch, Late 2013 model, running 10.11.1. The problem initially manifested as drives seeming to spontaneously disconnect. Then, things got worse when I could no longer connect my iPad (it would cycle through mounting and not mounting). This was all on the right side USB (near the HDMI jack). After getting my machine back today (with a new motherboard), the problem persisted so I began more methodical testing with two USB 3.0 drives, an iPad mini 2, and a powered hub. EVERYTHING works fine on an older MacBook Pro running El Capitan--it all mounts and all is welll, albeit at USB 2.0 speeds. On my 2013 model, though, one USB drive simply will not mount--using different cables, different USB ports, using the powered USB 3.0 hub--nothing. One USB drive is fine on the hub, fine on the left USB port, but mixed responses on the right USB port, especially after sleeping. The iPad cycles through mounting and dismounting when plugged directly into the right USB port, but mounts fine on the left USB port, so long as there is no prolonged (>5 min) sleep period. It also mounts fine via the powered hub. So, I guess I'm pretty convinced that Apple is trying to eek out longer battery life (or energy consumption) benchmarks at the expense of adequately supply power to peripheral ports, or at least to the USB ports. Very frustrating!

I'm seeing consistent issues with El Cap on my MBP 2013, too... even now, just about in December.

When it goes to sleep, my usb keyboard will not wake it.  I have to open the laptop and close it again, and then usb starts responding any my monitors will turn on again. 

Also, It's been consistently failing to restart the SD card controller after sleep.  It doesn't even show up as a device in the system after sleep some times.  Putting it back to sleep and waking some times will recover it.  Kext load/unload of the sd card module doesn't work when this is happening.

This fix worked for me:

Here are the instructions on resolving your issue with the iPhone not charging when closing the lid of your Macbook.

1. Go to System Preferences/Energy Saver

2. uncheck Put hard disks to sleep when possible on both the Battery and Power Adapter tabs

3. Shut down computer

4. Restart.

***Optional.***You can reset the SMC (System management controller) if these steps do not resolve it via article HT201295. (Just search that number in google search. )

I have the same problem as everyone else - power to the USB ports on my MacBook Pro is cut in half, so any of the external USB drives that are not SSD do not work.  They do not even mount and are not visible in the Disk Utility.  If I give them external power, I can get to them, but moving data (for example backup using Time Machine) is incredibly slow.  I waited until Dec 17th to upgrade to El Capitan, and I regret it!  We need a fix, quickly !!

Having the same problem, and I have only just installed 10.11.2 on my MacBook Air. Definitely seeing reduced current, and at least one port shuts down still. Can Apple please respond to this thread with some information? This is ridiculous.

It is DEFINATELY underpowered USB ports!  If I plug my external drives into power and then into the port, they at least work, albeit a LOT SLOWER than before I "upgraded" to El Capital.  Big mistake upgrading and nearly impossible to downgrade at this point.  APPLE PLEASE FIX THIS !!

Same problem and I'm annoyed with Apple Support, who basically told me "Sorry, there is nothing I can do."

If shutting off USB power when sleeping is to save power, I can possibly see that argument, but shutting power off to USB when the Power Adapter is plugged in little sense to me.  In effect, this USB power issue prevents me from using my Macbook Pro as a desktop replacement.

Just adding my voice to the choir to see this thread grow and grow.  I see three problems

1.  Possible corruption of data with repeated disconnects (AppleCare suggested that that I disconnected the drive every night)

2.  Preventing computer from sleeping will likely reduce the longevity of Macbook and external drives. (Not a long-term solution)

3.  "Wake for network access" doesn't seem to work with USB to ethernet dongle with USB ports that have no power

One question:  AppleCare said I can't go to previous OS since my Macbook Pro shipped with El Cap.  Is this right?

Does anyone have the same experience with Thunderbolt ports doing the same thing? While an imperfect (and costly) solution, I could switch to Thunderbolt hub if it worked.