I don’t think that there is a way to do this. All that shortcode does is generating some HTML code and putting it as content.
But… there is a workaround you can use. Your shortcode can generate only a placeholder for its content and then you can use AJAX to populate it with real content. It’s a pretty common practice to deal with cache in WP – for example WooCommerce uses exactly this method for its cart.
PS. If you’re using W3TC you can set a list of pages that shouldn’t be served from cache.
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