Berbatov was seen holding his back during periods of the first half, and it was expected that the striker may be substituted at half-time.
However, Berbatov had an injection during the interval, and was able to score Fulham's third goal before Reading equalised in injury-time.
"It was difficult, because I think Berbatov broke his rib," Jol said.
"We thought he may come off at half-time, but he had an injection to carry on."
Jol was frustrated that his side could not hold on for the victory, saying: "It is definitely two points dropped. We should have won the game.
"When you score three goals away from home, against Reading, you deserve to win.
"We were the better team, we kept the ball and had more purpose to our play. But you have to exploit that."