The statue was erected behind the Hammersmith Stand in April 2011 at the request of former owner and chairman Mohammed Al Fayed, who was close to Jackson.
Some Fulham fans fiercely opposed the decision to erect the statue, but Al Fayed responded by telling them to "go to hell".
Al Fayed sold the west London club to Shahid Khan in July and, after consulting with supporters, the American businessman decided to pull the 7ft 6in statue down.
On Wednesday morning four workmen cut the sculpture free from its plinth and returned it to Al Fayed.
It is understood that the Egyptian millionaire has received offers for the statue and could sell it to raise money for charity.
Jackson, who died of an overdose in 2009 at the age of 50, watched Fulham play Wigan at Craven Cottage as a guest of Al Fayed 10 years earlier.
Al Fayed's successor defended the decision to remove the statue last week.
"Our supporters' views on the statue have been made clear," Khan said.
"I respect Mr Al Fayed and know he had good intentions in paying an individual tribute. However, the removal of the statue is the right thing for Fulham Football Club."
Fulham say the statue does not form part of their plans to revamp their stadium, which lies on the banks of the River Thames.
- Sports & Recreation
- Mohammed Al Fayed