I encountered this bug after uninstalling GeoIP, when I had removed the reference to it from [but not PluginsInstalled or [Plugins_Tracker]. Obviously it should error at this point, but it presumably shouldn't be the error logger that breaks!
PHP Fatal error: Class 'Piwik' not found in /home/{user}/public_html/piwik/core/PluginsManager.php on line 439
Line 439 is a call the the Piwik:log function, logging that the plugin cannot be found.
Piwik::log("Unable to load plugin '$pluginName' because '$path' couldn't be found.");
I would vote for the priority being set higher. I encountered the same bug and fixed it like suggested: removing "GeoIP" from the config.ini.php altogether. Should the extension be uninstalled during an upgrade script? If so, this was not the case for me.
Note that no logging is done while this error occurs.