You can un-check the build automatically in Project menu and then build by hand by type Ctrl + B, or clicking an icon the appears to the right of the printer icon.
You will need to go to Project->Clean...,then build your project. This will work, even when your source code does not contain any main method to run as an executable program. The .class files will appear in the bin folder of your project, in your workspace.
In the case that you delete your .class file in Eclipse and then try to build it again from the .java file it will do nothing. If you try to run the .java file without the .class file you will get an error that it can not find the main class.
You will either have to change and re-save the .java file then build it again, or else you have to run Clean on the project then build again.