You will need to write a custom menu walker.
See this code for the walker. (Or do a search for “Bootstrap Menu Walker”.)
Then use:
wp_nav_menu( array(
'menu' => 'header',
'menu_class' => 'nav nav-pills',
'container' => 'nav',
'container_class' => $classes,
'fallback_cb' => false,
'depth' => 2,
'walker' => new Bootstrap_Walker_Menu_Nav(),
'theme_location' => 'header',
'echo' => false,
));