Can we use the multiple databases system concept in a single web application?
I don't see why not.  You would just create two data sources and potentially two data access layers if you want to take it that far.  At least for .Net/C#/VB.Net this wouldn't be a problem.
I'm not sure I understand the benefit in this case but if you feel you have a good reason to separate the database, there's no reason it can't be done.