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.
Jol, a former Dutch international, established his coaching credentials with Roda JC and RKC Waalwijk in the Netherlands before moving to Spurs in 2004 as assistant to Jacques Santini, whom he replaced as manager later that year.
A popular figure at White Hart Lane, who had also spent three years playing in England with West Bromwich Albion and Coventry City, Jol led Spurs to successive fifth-place finishes in 2006 and 2007 and took them into the UEFA Cup.
However, he was sacked three months into the 2007/08 season and replaced by Juande Ramos.
Jol then spent two years at Hamburg SV before moving to Ajax in 2009.
He was in talks about a possible move to Fulham last year after Roy Hodgson left for Liverpool but stayed with Ajax, only to resign in December.
