You need to check config files loaded by PHP, because the fact extension is intalled does not automatically mean it cannot be disabled. So inspect:
Loaded Configuration File => /etc/php5/cli/php.ini
Scan this dir for additional .ini files => /etc/php5/cli/conf.d
Additional .ini files parsed => /etc/php5/cli/conf.d/05-opcache.ini,
/etc/php5/cli/conf.d/10-pdo.ini,
/etc/php5/cli/conf.d/20-json.ini,
/etc/php5/cli/conf.d/20-readline.ini
especially this one:
/etc/php5/cli/conf.d/20-json.ini
and uncomment the zend_extension=...
line in case it is commented out (or not present)
EDIT
I just realised that what you included in your question as php state info may not come from the same PHP your Eclipse is using. To ensure we are not looking at something different, run this script via eclipse
<?php
phpinfo();
and see what you got JSON related there (if there's JSON extension listed). Also check what php.ini
is listed.