By definition, custom site  defintions only affect newly created  sites.
What kind of changes are you trying to enforce?
I have made  changes to sts  site
definition, it is working  fine, but only on the newly created sites. How to
enforce existing  sites to use the customized  site definition? any way?

This kind of makes senses since the template page is unghosted, but is there a
way to get around?

The change I made  is to use customized  master page instead of global one. The
changes include left navigation(quick launch) and top link tabs and other
navigations.

Some site  definition changes affect existing  sites, others do not.
If you modify ONET.XML or any list definitions, those are recipes for
site creation, and therefore do not change existing sites. However,
if the site definition  deploys files referenced from the file system,
like default.aspx, or master pages, these will update all existing
sites for which those files are not customized  (unghosted). So if
you want your existing sites  to be affected, you may need to reset
those pages to the site definition in SharePoint Designer.

It's generally better not to change OOTB site definitions. You can
copy them to a new definition and deploy to new sites. As for
existing sites, changes are usually better made  as features that can
be stapled or just activated on existing sites, rather than updating
the existing definition.