As per rule to get this benefit... if 'Married Filling Jointly' then both must have SSN.

Now how can I get this benefit as...

1) When returned was filed spouse was not having SSN and hence applied for ITIN
2) I already got return amount
3) Now both has SSN

Please advice.

Call IRS and find out.

See:
Basic Information on the Stimulus Payments

It says:
Not eligible at the current time? If you're not eligible this year but you become eligible next year, you can claim the economic stimulus payment next year on your 2008 tax return.

So now that you both have SS numbers, it seems that if you are ineligible for a payment based on your 2007 return, you should be able to claim it next year.

You can amend your return with the SSN; that should make you eligible for the next stage payment of the stimulus checks, which I believe is in September.