Hughes resigned after one season last Thursday amid media speculation linking him with the vacant post at Aston Villa and 55-year-old Jol was confirmed as his replacement on the club's website five days later.
The Dutchman, who managed Tottenham Hotspur between 2004 and 2007 and who stepped down as boss of Ajax Amsterdam six months ago, has signed an initial two-year contract with Fulham with the club having an option to extend for a further year.
"I am very happy to join Fulham, a wonderful traditional club," Jol said in a statement on the website.
"It is a club with good, solid foundations and a great fan base. I am looking forward to being part of the Fulham family and thank the chairman for the trust he's shown in me."
Fulham finished eighth under Hughes and will play in next season's Europa League after qualifying via the Fairplay table.
