Dubois, 22, has been widely tipped to emerge as a contender for a world title and dominated his Japanese opponent, flooring him with a jab in round two.
Fujimoto got back to his feet but a brutal right hand left him in need of medical attention on the canvas.
"I landed a sweet shot and that was goodnight," said Dubois.
"I just thought after the first couple of shots I had to pace myself and let him come to me. I knew I had the power and was really confident in what I was going to do."