How to wait for user input on JavaFX application thread without using showAndWait?

You can do so by using Platform.enterNestedEventLoop to pause the execution of the event handler and Platform.exitNestedEventLoop (available since JavaFX 9) to resume the execution:

private final Object PAUSE_KEY = new Object();

private void pause() {
    Platform.enterNestedEventLoop(PAUSE_KEY);
}

private void resume() {
    Platform.exitNestedEventLoop(PAUSE_KEY, null);
}

Platform.enterNestedEventLoop returns when Platform.exitNestedEventLoop is called with the same parameter passed as first argument.