The 32-year-old was left out of the Cottagers' 2-0 defeat at Manchester City on Saturday, with Jol using Kieran Richardson at left-back before bringing on Matthew Briggs.
Riise has not started a game for the south London side since Boxing Day, but the Fulham boss insists the Norwegian had just been given the weekend off.
|CUP RUN COTTAGERS
|5/1||Fulham are 5/1 to make it to the fifth round of the FA Cup with William Hill|
"I wasn't happy after the Liverpool game, when Stewart Downing scored his first goal since he joined Liverpool and John was playing against him, so I tried something to freshen things up and alert him. I want to challenge all the players."
Riise’s brother, Bjorn Helge, recently claimed that his sibling came to blows with the Fulham manager, but the 57-year-old played down reports of any such altercation.
The Dutchman added: “John Arne Riise is a fantastic boy so he wouldn't ever come up with this sort of thing.”