No, domain mapping is not built into the WordPress core. It might be sometime in 2016.
I was going to guess that what you are doing is site1.example.com and site2.example.com (as a subdomain installation as you mentioned) or in a subfolder setup, example.com/site1/, example.com/site2/ .
This would be simply multi-site. No domain mapping needed.
But then I noticed you said you "changed the subdomains to actual tld domains". That does need the Domain Mapping plugin (or serious server configuration skill to do it manually).
I think what is going on is with "i have disabled domain mapping plugin". If you installed the plugin properly, you moved files into specific locations, where they get run Always; all you did was disable the management screen.