The club announced Rene Meulensteen would take over responsibility for the first team, stepping up to the top job having only been recruited last month as head coach to assist Jol.
Fulham were beaten 3-0 at Upton Park and after 13 games of the Premier League season they stand 18th, inside the relegation zone.
Fulham chairman Shahid Khan said in a statement on the club's website: "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."