The hosts took the lead through a Gary Madine penalty in the 50th minute and stubbornly refused to relinquish their advantage to the disappointing Cottagers.
The Dutchman left out the likes of Moussa Dembele, whom the club later confirmed is having a medical ahead of a £15 million move to Tottenham, and Costa Rican forward Bryan Ruiz was forced to withdraw from the starting XI after an injury in the warm-up.
|8/1||Fulham are 8/1 with Bet365 to lose 1-0 to West Ham in their next match|
Jol told the club's official website: "We made five changes but we had enough to cause them problems so it was disappointing.
"We mixed it around a little but we struggled to get going in the first half. Then we lost the goal and we stepped up towards the end but we just didn't have enough."
The absent and soon-to-be-sold Dembele has also been linked with Real Madrid and Manchester United but, as Goal.com exclusively revealed on Monday, Spurs have moved into pole position in the race for his signature.