The five times world champion started on pole position but finished second in Melbourne last Sunday after Finnish team mate Valtteri Bottas seized the lead off the line and went on to win by 20 seconds.
Mercedes said after the race that part of the floor on Hamilton's car was missing, with Vowles providing more detail on the team website.
"On inspection of Lewis's car after the race, we noticed some damage over what we call the tyre seal area," he said.
"That area is quite sensitive aerodynamically; it's both for downforce and also for balance of the car. And we believe we sustained it during the course of the race while riding over some of the kerbs."
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Vowles said Hamilton's progress during the race was also hindered by having to manage the tyres significantly after an early pitstop to cover the threat posed by Ferrari's Sebastian Vettel.
"That floor damage wouldn't have helped," he said. "It would have caused the rear to be more unstable than it normally would be, and he did a fantastic job bringing that car to the end of the race."
Vowles praised Bottas for being "on it all weekend", with a perfect start and then leaving enough tyre performance to set the fastest lap.
(Reporting by Alan Baldwin; Editing by David Goodman)
