What Jesus said is true, but what if you need need the singleton bean to acquire a new instance of the prototype bean repeatedly at runtime? You can do this as well using method injection. The following (from spring docs) shows a singleton bean 'CommandManager' which through method injection grabs a new instance of the prototype bean 'AsyncCommand' every time at runtime. Note I showed you the java config way because I prefer it, but you can find the XML way as well in the spring documentation. The trick to the way this works is the way that createCommand() is overridden.
Hemant brings up a good point and I has thought of bringing it up as well but I did not mention it since the asker specifically targeted singleton and prototype beans. AOP proxy is more geared towards session or custom scoped beans.
From the docs you referenced.
But that is not to say that you can't use it with a prototype bean. Rather than putting AsyncCommand as a bean as I did in the first example you would slap an @Component on the class and add @Scope(proxyMode = ScopedProxyMode.TARGET_CLASS, value = "prototype")
*Note to proxy your class in this fashion you need CGLIB on your classpath but I always have that anyway since I use java config.
The XML way is clearly shown in the doc link Hemant gave, I showed the annotation based approach just as an alternative.
This is a nasty example but I think it illustrates the point consider the following.
The class Singleton is a singleton the new operator is only called once ever. After that the same instance is used by calling the getInstanceMethod. Despite that fact SomeObject is new every time the instance is retrieved.