Well if you can get the canonical tag in the head section this would certainly be preferred. It sounds obvious that you are dealing with a dynamically generated page rather than a static page or you would certainly be able to insert the tag with any average web editor.
I don't know that too many people would have ever tired this to honest with regard to placing such a tag in the body section. I'm gathering that you need the tag based on numerous results for the same product page, such as page 2, page 3 an so on right.
What type of shopping cart are you using? This can help others answer your question as they may be using the same cart and as such it might be an easy answer. If you could supply a link and/or cart type I might have more insight.