How to let Google show my primary domain instead of secondary?

How to let Google show my primary domain instead of secondary?

I've two domain names for the same website. E.g. primary.com and secondary.in
I've used URLRewrite Filter to redirect from secondary.in to primary.com
everytime someone hits secondary.in. This is the rule:
<rule>
<name>Redirection</name>
<condition name="host" operator="equal">www.secondary.in</condition>
<from>^(.*)</from>
<to type="redirect">http://www.primary.com$1</to>
</rule>
This works fine. I also have both the domains pointed to my Amazon Elastic
Beanstalk domain through CNAME.
The problem is Google shows secondary.in in the results page. How to stop
that? How to make Google display primary.com instead?
I have a Google Webmaster account for primary.com and not for
secondary.in. Can someone please guide me. I'm really stuck.
EDIT
I've been using WWWIZER to redirect my naked domains to www. But some
sites say that their ip 174.129.25.170 is blacklisted. Can that be the
cause?