Andy Roeser's leave is effective immediately and will "provide an opportunity for a new CEO to begin on a clean slate and for the team to stabilize under difficult circumstances," league spokesman Mike Bass said in a statement.
The league announced last week that it was working with the Clippers to appoint a new CEO.
Roeser, 54, is one of the league's longest-tenured executives, having just completed his 30th season with the team. He was the first to publicly defend Sterling in the wake of the scandal that erupted last month.
"Sterling has not spoken publicly about the scandal. But legal experts have said they do not expect him to give up ownership of his team, which he purchased in 1981 for $13 million when it was based in San Diego, without a fight.
"Experts have estimated the franchise, which moved to Los Angeles in 1984, could now be worth as much as $1 billion."