Ajoutez dans le header.tpl ce petit bout de code:
<!-- canonical -->
{if $page_name == 'index' or $page_name == 'search'}
<link rel="canonical" href="{$base_dir_ssl}{$lang_iso}" />
{elseif $page_name == 'category' or $page_name == 'best-sales' or $page_name == 'cart' or $page_name == 'discount' or $page_name == 'manufacturer' or $page_name == 'new-products' or $page_name == 'prices-drop'}
<link rel="canonical" href="{$base_dir_ssl}{$request_uri|substr:1|regex_replace:'/\/(.*)/':''|regex_replace:'/\?(.*)/':''}" />
{else}
<link rel="canonical" href="{$base_dir_ssl}{$request_uri|substr:1}" />
{/if}
<!-- /canonical -->