Yes, you can use functions from plugins in your theme. Please use the function_exists() function to make sure that the function does exit. I used the Breadcrumbs Plus in one of the themes like this:
<?php
if (function_exists('breadcrumbs_plus'))
{
$breadcrumb_options = array(
'prefix' => '<div id="breadcrumb">',
'suffix' => '</div>',
'title' => 'Du er her: ',
'home' => 'Forside',
'sep' => "https://wordpress.stackexchange.com/",
'front_page' => false,
'bold' => false,
'blog' => __('Blog', 'rev'),
'echo' => true
);
breadcrumbs_plus($breadcrumb_options);
}
?>