How to use pip after the OS X El Capitan upgrade?
A quick solution is to use homebrew to install python into /usr/local/bin so that your pip can run against a user-modifiable python framework.

brew install python
pip --version


Disabling System Integrity Protection is also an option, but I don't recommend that for anything but professionally managed and fire walled servers where you have the manpower to manage intrusion detection or if you are a developer/sysadmin and need to test things with and without SIP.

ls -lO /System/Library/Frameworks/Python.framework/Versions/2.7/
csrutil status


You will see that the restricted flag is set which cannot be removed even as root while SIP is engaged.

Using homebrew makes it possible to manage pip and python separately than the system provided version. As a bonus, the homebrew framework is designed to ease maintainance and patch/chores via automation.