Jol's side had not won in seven games but took the lead through a deflected Steve Sidwell effort and secured a much-needed three points when Hugo Rodallega headed home just nine minutes after Hatem Ben Arfa had levelled for the visitors.
Berbatov should have scored at least once on the night but his close control and first touch drew constant applause from the majority of the fans inside Craven Cottage.
Jol, too, was impressed with the performance from the man he signed from Manchester United in August.
"We had that spell (of poor results) that started against Sunderland with the red card and two big injuries for us," he said. "That was very disappointing for us and then after that we couldn't play Bryan Ruiz - he was out for four weeks for us.
"I was happy that Berbatov, after talking to him, could fill in that role (behind the striker). It was vital, he didn't score so that was disappointing, but on the other hand he linked us up and kept the team together - I was very happy with him."
Berbatov's arrival was hailed as something of a coup for Jol and according to the Dutchman, both he and his squad are aware of how important the former Spurs striker is to Fulham.
"The good thing about my squad is that they realise Berbatov is an outstanding player," he said.
"For me the most important thing is that after losing (Clint) Dempsey - who is making the difference for Spurs now, as well as (Mousa) Dembele plus Danny Murphy and Bryan Ruiz (through injury) I'm very happy that he came to this club because otherwise maybe we could have ended up with a little problem."
And Jol reckons his side were worthy of the win.
"We couldn't finish them off and then they scored that goal with Ben Arfa - he is a quality player and he scored," he said.
"But to be fair we have got three or four opportunities and, Berbatov had maybe three of them, to score the 2-1 before that.
"You could say we didn't score at the right moment but if you see the first goal and the second goal, in hindsight it was just enough because we deserved it."
Newcastle boss Alan Pardew, who has not seen his side win away from St James' Park since May 2, was also full of praise for Berbatov's performance.
"He was special tonight [Monday]," he said.
"Everything he seemed to pluck out of the sky, everything seemed to die on his toe - he was a real problem.
"I thought we did much better in the second half with him but he is a class act when he is in the mood and when the TV cameras are here and he is a real problem."
The visitors came into the game in the closing stages of the first half and Pardew felt his side were on top after Ben Arfa drew Newcastle level.
But the Magpies' manager was not impressed by his team's defending of a Fulham free-kick that allowed Rodallega to score a simple header, a goal which earned Fulham the win.
"Second half we had the game by the scruff of the neck really, the goal was a soft goal," he said.
"We gave away a cheap free-kick and then we didn't defend that situation well at all and have come away losing a game we should've got something out of.
"We just didn't defend it well it I'm honest, we are going to have to be better - we can't concede soft goals at this level. To win that game we needed to score three at Fulham and it is really difficult to do that.
"Of course it is very, very disappointing because I believe we have an honest set of players and we work on situations and really for us it is a poor goal, I can't so no more than that really."
Newcastle have now lost five out of their last six league games and Pardew admitted times were tough for the club.
"I'm worried in so much as we are not picking up enough points, that is pretty evident," he said.
"Although the performances against Stoke, Wigan and today [Monday] have improved, it is a worry we don't have enough points on the board."