If the same content is accessible from two or more different URLs, that is indeed duplicate content.
When you say you "rewrote" your site pages from .php to .html extensions, how exactly did you accomplish this? By that I mean: did you physically recode the pages so that the old .php pages now exist as both .html versions and .php versions? Or was this something you accomplished through the back-end of a content management system (such as Wordpress)?
If you physically rewrote the pages and there are now two copies of each page (one .html and one .php) sitting on your web server, you should implement a 301 redirect from the old version of the URL to the new. Depending on your web hosting company, you may be able to do this through their control panel, or you may need to update your .htaccess file to include the redirects. Your hosting company should have instructions in their help section or their support staff should be able to talk you through how to set up these redirects.
Once the redirects are in place, you can safely delete the old .php versions of the pages.
On the other hand, if this "rewrite" was done through the back end of a content management system, we'd need to know which CMS you were using. Typically, pages generated by a CMS would not be available under two URLs in this scenario, so in that case it sounds as though there might be some problem with the configuration. Without knowing the CMS in use, it's impossible to troubleshoot.