The Nets announced Levy, a former president at Turner Broadcasting, and the franchise "mutually agreed to part ways."
Oliver Weisberg was named the Nets' interim CEO.
"I want to thank David for his collaboration over the past several months and wish him well in his future endeavors," Weisberg said in a statement. "As we enter an exciting next chapter of our organization, it's important that ownership and management are completely aligned on our go forward plan.
"We are proud of the culture of the Brooklyn Nets under the leadership of general manager Sean Marks and head coach Kenny Atkinson, and we look forward to continue bringing the best experience to our fans."
The Nets hired Levy on Sept. 18, the same day Tsai finalized his purchase of the team and Barclays Center. Levy worked closely with the NBA while employed at Turner and was entrusted with overseeing all business, revenue, strategy and operations for the Nets.
"David Levy is a respected media executive and a friend," Tsai said in a statement. "Truly appreciate his efforts in the past few months. I wish him well in his next endeavors."