Mladen Petric returned from injury and scored the opening goal from the penalty spot, but Sergio Aguero and Edin Dzeko struck to seal three points for the defending champions.
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"Petric did well, coming back after three or four weeks out," Jol told reporters. "But of course Berbatov has qualities that can make a difference against a team like Manchester City.
"Someone told me he's played 10 times against them and lost only once which gave me confidence. So it was very disappointing for us when he got his injury on Thursday."
The Bulgarian is currently sidelined with a hip injury and looks likely to miss Fulham's next match against Southampton.
Jol was frustrated to see his side concede the points after taking the lead and felt that they edged too far towards accepting a draw instead of attempting to win the match.
"We went 1-0 up against the defending champions but in the end got nothing," he bemoaned. "We needed a result to justify our first-half performance.
"For an away team they certainly play with confidence and that is the sort of quality you need to win the title. As for us in the second half we played almost for a point - and you can't do that at home."