The Cottagers have been on a disappointing run of results and currently sit in the relegation zone of the Premier League.
Jol's side were beaten by West Ham United on Saturday, as the Hammers ran out 3-0 winners at Upton Park.
Fulham chairman Shahid Khan released a statement saying: "Today I spoke with Martin to thank him for his efforts on behalf of Fulham Football Club over the past three seasons and, in particular, since my becoming chairman earlier this year.
"Martin was very gracious and I appreciate his understanding of the situation. There is no question Martin is an excellent football man and he has my utmost respect for the commitment he made to our club.
"However, our poor form and results this season are undeniable, and Fulham supporters deserve better. With more than half the season still ahead, an immediate change was necessary."
Rene Meulensteen will take over as first-team manager on a permanent basis.