I accidentally deleted the App Store.app
Once, I also deleted the Mac App Store from my MacBook Pro running OS X Snow Leopard. I fixed it by downloading the Combo update. So you can also try downloading the COMBO update for 10.9.5 from here : https://support.apple.com/kb/DL1760?locale=en_US. 

Combo Updaters are your best bet since if anything changes within the app between 10.9.0 and 10.9.5, then the app will be in the package.

However, since this app isn't supposed to be deletable, you might want to run a full reinstallation of the entire OS. That will perform a much better check on things and permissions in case you have further damage than just that one app being deleted. Start with the combo and try the full install if you still have issues or doubts.

Lastly, now is a very good time to make a back up of what you have before you install anything.