I have this set in my config.yml:

framework:
    templating:
        engines: ['twig', 'php']

When I try this in my controller:

$this->render('@MyTools/Tools/index.html.twig');

... I get the following error:

Template name "@MyTools/Tools/index.html.twig" is not valid (format is "bundle:section:template.format.engine").

Removing 'php' from the engines solves the problem and using the old template name style ('ToolsBundle:Tools:index.html.twig') also solves it.