How to use Bootstrap 4 flexbox to fill available content?

Your component is wrapped into a <flex> element that needs the same flexbox styling to stretch vertically as well, allowing it's content to stretch with it. So adding class="d-flex flex-column flex-grow" to the <flex> will work. Here's a working fork of your plunker example.

Update Bootstrap 4.1.0

The flex-grow-1 and flex-fill classes are included in Bootstrap 4.1.0

Update Bootstrap 4.0.0

Add a flex-grow class like this:

.flex-grow {
    flex: 1 0 auto;
}

Then, the utility classes can be used for the rest of the layout:

 <div class="d-flex flex-column h-100">
    <nav class="navbar navbar-toggleable-md sticky-top bg-faded">
        <a class="navbar-brand" href="#">
            <h1 class="navbar-brand mb-0">My App</h1>
        </a>
        <ul class="navbar-nav">
            <li class="nav-item"><a class="nav-link">Item 1</a></li>
        </ul>
    </nav>
    <div id="outer" class="d-flex flex-column flex-grow">
        <div id="one" class="">
            header content
            <br> another line
            <br> And another
        </div>
        <div id="two" class="bg-info h-100 flex-grow">
            main content that I want to expand to cover remaining available height
        </div>
        <div id="three" class="">
            footer content 40px height
        </div>
    </div>
</div>

https://www.codeply.com/go/3ZDkRAghGU

Here's another example with on Bootstrap 4.3.1 that has a navbar, sidebar and footer with scrolling content area: https://www.codeply.com/go/LIaOWljJm8