It was reported earlier this week that the 19-year-old summer signing had been reprimanded by Jol for his penalty miss against Chelsea in the Carling Cup last month.
Kasami was reportedly fined £500 for the incident, which subsequently led to unrest within the Fulham team.
The Switzerland Under-21 international has on Wednesday moved to quash such speculation and apologised to Jol for his actions at Stamford Bridge.
"In the heat of the battle at Stamford Bridge I felt confident that I could score when we were awarded a penalty against Chelsea," he told www.fulhamfc.com.
"I wasn't fully aware that Orlando Sa was the designated penalty taker for this game, and it was my desire to help my team and that resulted in me stepping forward.
"In hindsight I made the wrong decision and I apologised to the manager immediately after the game, and we agreed it was a miscommunication.
"Any subsequent action taken against me is a confidential matter between me and the manager, and I am satisfied with the outcome and have no issues about it.
"As for this matter causing any unrest in the camp, these reports are utter rubbish and I am most disappointed that after such a fantastic win on Sunday, this story is making the wrong kind of headlines."
Fulham defender Brede Hangeland also expressed his disappointment at the story, adding on the club's official website: "I haven't even spoken to Pajtim about this, so it's news to me that I'll be discussing his fine with the PFA."
Jol's relationship with Fulham players has come under increasing scrutiny in recent times and last week he was forced to play down talk of a bust-up with Bobby Zamora.