The Cottagers looked on their way to a point at St James' Park before Hatem Ben Arfa fired home with five minutes left.
Jol feels that Fulham should have at least held on for a point.
"I really thought we should have finished them off, our midfield was good but up front we should have taken advantage - that is what we did against Sunderland," Jol told Sky Sports.
"We played with two front players and we had Berbatov dropping and he was pulling the strings and we should have done better.
"But to be fair they put a lot of crosses in and we can't afford that but I think if we had scored we would have got more room up-front from that."
Fulham lost Sascha Riether to injury in the second half and Jol felt his loss allowed Newcastle to push on more.
"He is a very good full-back and he came off and we didn't have a lot of options, but they still got these crosses in and we have to get better - first half we had 50 per cent possession.
"The Arsenal defeat was disappointing and today we should have had a point or a win and I think we could have done it."
Jol did admit that Fulham want to bring in one new player before the close of the window, adding: "I think we will be, no more than one."
Jol did praise recent signing Scott Parker as he looked a real spark in Fulham's midfield.
"He is a terrific player and under pressure he turns and he is a really good player and that is what we needed," he continued.