I want to have a backup from my environment in sharepoint, I am doing database backup from SQL, but I want to make the process automated as I need to do scheduling at the end of each week. I started using backup-spsite, as this is a good way for me to get backup of all site collections in my web applications. But it doesn't take the web application itself. 

Is there a way to automate it that it takes web application as backup instead of site collection?

Did you have a look at this: https://technet.microsoft.com/en-us/library/ff607881.aspx

You're best choice is to use backup-spfarm, as having backup from database will take only 1 web app for you, so you need something with bigger scope to take all web apps.