Fox confirmed Lythgoe's exit yesterday (June 9) after reports emerged that he and fellow producer Ken Warwick had been fired from the series.
The TV mogul has now said that it was a "tremendous honour" to work on the show and that he is "truly saddened" to be leaving.
He said in the statement: "It has been a tremendous honour to launch and build American Idol over the course of a decade and to see it recognised with 51 nominations and six Emmy Awards, including the Academy's highest honour, the Governors Award.
"To be a part of the spin-off programme Idol Gives Back was incredible. As well as raising nearly $200 million for various charities, it was a personal life-changing experience for me.
"It also provided me with the opportunity to produce and direct a magical sequence with Celine Dion together with Elvis Presley. This continues to be one of the highlights of my entire career.
"Over the years, I believe we have changed the face of American television forever and eventually created a true global phenomenon. It has been inspiring to find and launch the careers of artists ranging from Kelly Clarkson, Carrie Underwood, Phillip Phillips and many more, spanning all musical styles and genres.
"I am truly saddened to be leaving a great team of friends and colleagues. However, at the end of the day, the most important thing is to maintain this incredible platform for America's young talent. This will only happen with the success of the programme.
"If the executives that are now in charge of American Idol believe that the ratings will improve with my departure, I have no complaints.
"It has been a great ride and I've loved every moment of it. After dedicating over 12 years to Idol, I look forward to continuing work on my beloved So You Think You Can Dance, which is going strong in its 10th season."
Lythgoe - who has worked on Idol since 2002 - previously tweeted his disappointment at the move, saying: "Just had 10 days in the Bahamas, rain everyday. I get back to the States and get fired. Sad! Monday we choose our top 20. I'll smile again."