From a Java server you can use the Firebase Admin SDK to send messages. From that documentation comes this minimal example:
// This registration token comes from the client FCM SDKs.
String registrationToken = "YOUR_REGISTRATION_TOKEN";
// See documentation on defining a message payload.
Message message = Message.builder()
.putData("score", "850")
.putData("time", "2:45")
.setToken(registrationToken)
.build();
// Send a message to the device corresponding to the provided
// registration token.
String response = FirebaseMessaging.getInstance().send(message);
// Response is a message ID string.
System.out.println("Successfully sent message: " + response);
Note that this sends a data message, so that will always be delivered to your code, where you can decide to display a notification or not. To send a notification message, which is what the Firebase console does, you'd use:
Message message = Message.builder()
.setNotification(new Notification("This is the title", "This is the body"))
.setToken(registrationToken)
.build();
Both of these send the message to a specific registration token, so only to a single device/app instance. This means you will need to maintain a list of these tokens, in a way that allows you to send the messages to fit your needs. E.g. a common way is to store the tokens per user. For an example of that, see the functions-samples repo. While this example is in Node.js, the same logic could be applied to a Java server.
Finally: you can also send message to topics. For an example of that (again: using a Node.js server), have a look at this blog post Sending notifications between Android devices with Firebase Database and Cloud Messaging.