// Removes default WooCommerce pagination.
remove_action( 'woocommerce_after_shop_loop', 'woocommerce_pagination' );
add_action( 'woocommerce_after_shop_loop', 'custom_woocommerce_pagination' );

//Adds FacetWP's pagination on WooCommerce archives.
function custom_woocommerce_pagination() {    
echo facetwp_display( 'pager' );}