"The transaction has been approved by the Barclays Premier League. Khan assumes 100 percent ownership of the club, debt-free, as of today," said a statement on Friday (July 12) issued by a spokesman for the new owner.
Last year the Jaguars signed a deal to play four games at Wembley Stadium over the next four years.
The Jaguars have struggled to fill their 67,000-seater home venue at times and are one of the NFL's weaker franchises.
The British Telegraph newspaper reported the deal would net Al Fayed up to 200 million pounds ($302.35 million).
The Egyptian businessman bought Fulham for 6.25 million pounds in 1997 and has bankrolled their rise from the third tier to the top flight.
"Now a new era dawns," Al Fayed said on the club website (www.fulhamfc.com).
"My time of serving as the custodian of Fulham Football Club would one day come to an end and I feel that time has now arrived.
"Fulham will be in very good hands with Shahid whose success in business and passion for sport is very evident. I ask everyone who loves Fulham and our Craven Cottage home to welcome Shahid as he begins his journey as the next guardian." ($1 = 0.6615 British pounds)