Lochte posted a time of one minute 41.92 seconds at the Sinan Erdem Dome. Paul Biedermann of Germany finished second in 1:42.07, while Conor Dwyer of the United States was third in 1:43.78.
Lochte won six golds and one silver when Dubai hosted the short-course championships in 2010. He won five medals at the London Olympics, including two golds.
Katerine Savard of Pont-Rouge, Que., was sixth in the women's 200-metre butterfly. She finished in 2:06.56, over four seconds behind Katinka Hosszu of Hungary.
Tera Van Beilen of Oakville, Ont., did not qualify for the women's 50-metre breaststroke final. She finished last in the 16-woman semifinal heat.
The competition runs through Sunday.
With files from The Canadian Press.