Trailing 2-1 as they sought the equaliser to reward their second half dominance, Spurs right-back Kyle Walker clearly handled the ball on the floor during a chaotic goalmouth scramble.
Referee Peter Walton failed to award the spot-kick and Jol insisted it was the wrong decision. "I felt we were a bit hard done by in the penalty situation. It was a penalty," Jol said.
Tottenham assistant coach Joe Jordan, standing in for manager Harry Redknapp as he recuperates after a heart procedure, disagreed.
"I don't think it was a penalty. There were a number of other areas where Fulham should look at. They had chances but they didn't take them," Jordan said.
It was a hard result for Jol to accept as Fulham staged a second-half onslaught that Tottenham were forced to ride their luck to survive.
Younes Kaboul's 57th minute own-goal was the direct result of relentless pressure from the home side and it was a cruel blow when substitute Jermain Defoe fired a third with virtually the last kick of the game.
"We deserved at least a point," Jol said. "I won't say we played them off the park because they're too good a team, but we played well and put them under pressure
"Everyone played their part. Today Tottenham had seven or eight attempts at goal and scored three goals. We had 28 attempts on goal but scored once. Tottenham were very efficient but in the second half they had two attempts on goal."
The defeat has left Fulham just one point above the relegation zone, but Jol is unconcerned by their position.
"We should have beaten Blackburn and Everton and deserved a point today. We're in a false position," he said.
Right-back Zdenek Grygera was carried from the pitch with an injury to his right leg that Jol described as "serious", but striker Andy Johnson should only be out for a week with his ankle problem.
Jordan acknowledged that Spurs had been stretched and remarked that the frantic final half hour will have given Redknapp a fright.
"We didn't expect to get a third goal the way the game went in the second half. It was just a case of hanging in there," he said. "In the first half we played well and deserved to be in front, but the second half was entirely different. We showed spirit and had to be resilient.
"Never mind the goalmouth scramble - that last half hour will have been a good test for Harry. If he passes that, which I'm sure he will, he may be back a little bit earlier. He's got another two weeks during the international break to recover."