The San Francisco Chronicle, citing team sources, reported owner Mark Davis was unhappy with how he and his late father, Al Davis, were portrayed in the SI story, leading to Gilbert's dismissal.
Sports Illustrated followed Mark Davis and general manager Reggie McKenzie over the course of a year for the story, which cast McKenzie in a favorable light but was particularly critical of Al Davis.
The Chronicle also reported that Gilbert hadn't been at the Raiders' facility since the SI story was published on April 18.
McKenzie brought Gilbert to the franchise after the two worked together in the Green Bay Packers front office.
Despite his firing, Gilbert thanked the Raiders for his time with the team.
"I'd like to thank Mark Davis for the honor of serving the Raiders, and Reggie McKenzie for hiring me," he said in a statement. "I leave holding my chin up, knowing I dedicated every waking hour to promoting a positive image for our team. The co-workers in my Raiders family are extraordinary; the camaraderie we built was really special.
"Talking to Raiders fans on a weekly basis, I learned first-hand that their passion and loyalty is unmatched. I have great respect for the team's rich history and took seriously the role of preserving it. Although disappointed that I can't remain on the ride, I wish Reggie and [coach] Dennis Allen absolutely nothing but success in a bright future."