I found the solution. It was just a symlink and original file was still alive in this directory:
/System/Library/Frameworks/JavaVM.framework/
So, simply put back the symlink using the following command:
sudo ln -s /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/java_home /usr/libexec/.
Update:
The System/Library/Frameworks
directory holds the framework files which provide interfaces needed to write software for Mac. You can learn more about this directory on official OS X Frameworks documentation.