Specifying Terminal-only mapping in Karabiner
My bad. I had to enable AXNotifier in Karabiner, and allow it access in System Preferences-&gt;Security &amp; Privacy-&gt;Accessibility. Hopefully the above will be helpful for others.

Sometimes posting a question helps resolving it by the very fact of posting it:)

UPDATE: Here is Karabiner's private.xml i'm currently using , in case someone would find it useful. It maps almost all of Ctrl+&lt;Key&gt; combinations, except for some that might still be useful (e.g. Cmd+Q, Cmd+N, Cmd+M).