This output shows, that php was not installed using a package manager on your system. Someone compiled and installed php from source. Therefore there is no way to update your installation using yum or rpm.
You have to download, configure, compile and install php again from source. Version 5.6.7 or higher is required to fix this vulnerability.
Another possibility is to delete the manually installed php version and reinstall a current version from a third party yum repository like remi (
Remi's RPM repository) or webtatic (
Webtatic.com). You have to check first, if the manual install was done for a special reason which can not be covered by the standard rpm packages.