Connect to your EC2 instance with Putty.

Open puttygen (PuTTy Key Gen)

Go to conversions->Import key->Select the key pair  .pem file you downloaded while launching instance.

Click on Save private key. It will save a .ppk file

Then open pageant click on Add key and select saved .ppk file It will ask for passphrase. Enter it and click OK.

Then close it.

Then open Putty 

Add your instance's EIP, Port 22,

Go To Data. For Ubuntu username is ubuntu. For Linux username is ec2-user

Go to auth under SSH and browse your .ppk file for key pair

Finally Go to session and click Save. And Click Open to connect to the ubuntu instance with SSH.

That's All. Now you have connected to your instance with SSH.