All you need to do is move the toolbar inside the md-sidenav-container. Ensure that the toolbar and the router-outlet are inside a flex div with column direction. Some CSS is required for adjusting the height, padding etc and set vertical overflow in the div enclosing the router-outlet. That will ensure the toolbar to be visible always when you scroll the content. 
The following works for me well.
(Note: I have used @angular/flex-layout, which makes flex layout easier. If you wish you can change it to regular flex css styling)
<div>
    <md-sidenav-container fxLayout="row" class="app-inner">
        <md-sidenav #nav class="app-sidebar-panel" mode="over" [opened]="false">
            <md-nav-list>
                <md-list-item>
                    <a href="#">Item-1</a>
                </md-list-item>
                <md-list-item>
                    <a href="#">Item-2</a>
                </md-list-item>
                <md-list-item>
                    <a href="#">Item-3</a>
                </md-list-item>
            </md-nav-list>
        </md-sidenav>
        <div fxLayout="column" fxLayoutAlign="start stretch">
            <md-toolbar class="app-toolbar" color="primary">
                <button md-icon-button (click)="nav.open()">
                    <md-icon>menu</md-icon>
                </button>
            </md-toolbar>
            <div class="app-route-content">
                <router-outlet></router-outlet>
            </div>
        </div>
    </md-sidenav-container>
</div>
The Style (SASS) required for this:
$app-toolbar-height: 48px !default;
$app-route-content-padding: 0.5rem !default;
$app-sidebar-width: 15.65rem !default;
// Important: This is required to override the
// default padding of md-sidenav-content.
:host /deep/ {
    .md-sidenav-content {
        padding: 0px;
    }
}
.app-inner {
    position: relative;
    width: 100%;
    max-width: 100%;
    height: 100vh;
    min-height: 100vh;
}
md-sidenav.app-sidebar-panel {
    overflow-x: hidden;
    width: $app-sidebar-width;
    box-shadow: 3px 0px 6px rgba(0, 0, 0, 0.3) !important;
}
md-toolbar {
    min-height: $app-toolbar-height !important;
    md-toolbar-row {
        min-height: $app-toolbar-height !important;
        height: $app-toolbar-height !important;
    }
    &.main-header {
        position: relative;
        box-shadow: 0 1px 8px rgba(0, 0, 0, .3);
        z-index: 1;
    }
}
.app-toolbar {
    position: relative;
    box-shadow: 0 1px 8px rgba(0, 0, 0, .3);
}
.app-route-content {
    overflow-y: scroll;
    padding: #{$app-route-content-padding} !important;
    height: calc(100vh - #{$app-toolbar-height} - #{$app-route-content-padding} * 2);
}
Hope this helps you.