Williams' song was pulled on Oct. 3 after an appearance on the Fox News program "Fox and Friends" in which he said President Obama playing golf with House Speaker John Boehner was "like Hitler playing golf with (Israeli Prime Minister Binyamin) Netanyahu."
Williams, 62, then called Obama and Vice President Job Biden "the enemy."
He apologized on Tuesday saying on his Web site: "Some of us have strong opinions and are often misunderstood. … They don't see eye-to-eye and never will. I have always respected the office of the president."
ESPN Thursday said it would no longer use Williams' 1984 hit "All My Rowdy Friends Are Coming Over Tonight," which had been adapted to open Monday Night Football on ABC and ESPN since 1991. Williams won Emmy Awards for the popular theme from 1991 through 1994.
"We have decided to part ways with Hank Williams Jr.," ESPN said in a statement. "We appreciate his contributions over the past years. The success of Monday Night Football has always been about the games and that will continue."
On his Web site Thursday, Williams said it was his decision to leave. He accused ESPN of "stepping on the Toes of The First Amendment Freedom of Speech, so therefore Me, My Song, and All My Rowdy Friends are OUT OF HERE. It's been a great run."