Papiss Cisse scored in the third minute of injury time at the end of the match, bringing the Cottagers' run of five games unbeaten to an end.
Jol's side rode their luck at times, with the hosts hitting the woodwork on three occasions and having claims for a penalty against Sascha Riether ignored.
Fine saves from Newcastle goalkeeper Tim Krul denied Stanislav Manolev and Dimitar Berbatov.
"I thought we controlled the game in the first half, it was almost perfect," said Jol. "We kept the ball and they could not dominate us, and the crowd were getting frustrated.
"At Spurs we limited them and then scored, and that was our intention today, and it almost came off. We didn't score, so 0-0 would have been OK as they kept on coming at us. Compliments to Newcastle, but we should have had a bit more today."
Fulham are still a point short of the 40 mark traditionally seen as being enough for Premier League safety, but Jol is confident that his side should not be looking over their shoulders.
"I don't think we have to look down, but it's disappointing not to get at least a point today."