One solution is simply don't auto-save. Only save content when the user intentionally chooses to do so.
On the web, auto-save functionality is not expected. Users typically expect to lose form information if they have not saved it.
Auto-save can be a nice feature when the situation calls for it, but you should only do when there is clear benefit and it doesn't add unnecessary complexity. The benefit generally comes with very complex forms or content editing (such as a CMS or email program), where the user is likely to be working on the content for a long time (without saving) and may leave and come back. For more standard forms and short content, it is unlikely to be very beneficial.
You need to implement something fairly complicated to handle this right (such as the suggestion by Jung Lee). Even then, if having two windows open is a common occurrence, the solution is likely to be unwieldy and confusing to users. The user will not expect auto-save to happen in a window they have only opened for viewing, and it will be annoying to have to decide between versions all the time.
In the absence of an auto-save feature, you could have a modal dialog warn the user if they are leaving a page with unsaved changes (as many sites, including Stack Exchange, do).
Another option to consider is opening pages for viewing only by default, and requiring an extra step to edit the content. This wouldn't eliminate the scenario, but it would make it rarer.