I had same problem. multisite feature and domain mapping work separately. so it’s not obvious what to do
you have multisite setup and domain mapping plugin installed and activated.
next you do this
1) create new site – subdomain.domain1.com
2) check that new site works
3) add new domain to domain mapping – domain2.com
4) hover over My Sites link at top of page
5) click on link to Network Admin / Sites
6) however over subdomain.domain1.com site links
7) click on edit
8) change domain to https://www.domain2.com
seems that you can’t create https://www.domain2.com directly. you are forced to create a subdomain of primary domain, then edit it and change to the new domain.