Interestingly, the Eclipse project has an SWT/JFace component/framework capable of displaying and generating (import/export) Graphviz's 'DOT' format, in pure Java:
ZEST (home page & download links)
See http://wiki.eclipse.org/Graphviz_DOT_as_a_DSL_for_Zest for usage examples.
Although ZEST is touted as an Eclipse plugin, it does seem that the DOT-manipulation API's can be used standalone and external to an Eclipse installation.
To clarify, the DOT functionality is a part of the ZEST 2 functionality, which itself is a sub-component of the GEF4 project.
Cheers
Rich
Update (May 2017) https://github.com/nidi3/graphviz-java