Hi Friends, 
Our marriage certificate  has maiden surname of my wife while she has her married surname in both her and my passport. Will it cause any problem when I apply for spouse visa for her to bring her to Germany. Kindly suggest how to deal with it. Thanks.

The name has to be identical in both passport and Marriage certificate. 

So, what is the solution now? Do they accept an affidavit saying both persons are the same. There is no way I can get a new marriage certificate. Or else, will a gazette notification of name chnage after marriage will do the trick??

Regards,
Shakti

You can change the name in passport using Tatkal. I dont know if its an option for you. 
I dont know about gazette notification. 

It is sufficient if you notify during the visa application that her name in the passport is different than the one on the marriage certificate.
There are fields in forms where you have to enter the actual surname and the old surname (maiden) if there is one, important is that the actual surname is the one in the passport. You should also consider a document proving the name change. I don't know if there is something like that in your country but when I naturalized, I was able to obtain such a document from the Bürgeramt for my wife as she wanted to take my name.

D.