The Remus had to be pulled out after two hours of a planned four-hour search because of worsening weather.
Luckily it had already captured the image police needed.
As they downloaded the material filmed underwater, police were able to identify Mr Thomas clearly.
Divers battled rough seas, pitch black water and 30cm of visibility to bring Mr Thomas back to his family.
It is presumed he drowned and the matter has been referred to the coroner.
"Without doubt if the navy's resources were not deployed as soon as they were, the body would not have been discovered," Mr Watson said.
"This joint defence and police operation showed an effective and efficient use of the government's resources available to obtain a positive result. In this case it was to return the body to the family to provide some closure."
THE REMUS
* Remote Environmental Monitoring Unit for conducting seabed searches.
* Can record black and white video for object identification.
* Can accurately search large areas of seabed quickly.
* Programmed onshore with the mission search grid and settings.
* Once a mission is completed, data from the Remus is downloaded and analysed.