I have 2 Web Application on the same farm and I have created 2 different content sources for them and crawled it.
How can I set the content source for respective search application.
You cannot set them to search application instead you should create search scopes which can be set to only one content source.
I believe you cannot associate a web application with a content source to fetch the search results. However, you can create a result source which can be mapped to a content source and then use that result source in your sites. Check this link
What I understood is that you have created 02 Search Service Applications and 02 Web Applications and you have configured Search to crawl those 02 Web Apps and now you want to associate those content sources to respective Web Apps. You can do this by modifying Service Application associations. When you create a Web App, you have an option to associate which Service Applications you want to consume. You can go and modify that to point to a particular Web App to at specific Search Service app which is configured to use specific Content Source.