Khan, who owns NFL franchise the Jacksonville Jaguars, bought the club from Mohamed Al Fayed last week, ending the 84-year-old businessman's 16-year association with the Cottagers.
Jol and club captain Brede Hangeland were flown from Costa Rica to Jacksonville to meet the new chief on Friday and the Dutch manager said he hoped to form a strong working relationship with his new boss.
"I'm delighted that Mr Khan has such a passion for football and has great ambitions for what we can achieve," Jol told Fulham's official website.
"A link with the Jacksonville Jaguars is very exciting and I know we're all looking forward to a successful future together.
"Mr Al Fayed was a fantastic chairman and I would like to publicly thank him for what he did for Fulham and the fans. Without him, the club would not be in this position so we all owe him a great debt of gratitude as he passes his custodianship over to Mr Khan."
American billionaire Khan, who did not get chance to meet Jol when he completed his takeover last week, will be present for the Cottagers' pre-season friendly against Deportivo Saprissa this weekend.
"The one regret from last week was leaving London without the opportunity to
meet with Martin Jol or Brede Hangeland," Khan said.
"I'd like to take this opportunity to publicly welcome Martin and Brede, thank them for their commitment to Fulham and wish them the best as we begin our 13th season in the Barclays Premier League."
Hangeland, who has been with Fulham since 2008, admits there was an air of excitement among the players as news of the takeover was revealed last week.
"Last weekend's announcement was greeted with much positivity and excitement," Hangeland said. "We want to make it a campaign to remember for everyone involved."