Zamora, who has reportedly fallen out of favor with Jol in recent weeks, has actually been suffering for "five or six weeks" with an Achilles problem, according to the Dutchman.
The former Tottenham boss, however, is hopeful that Johnson will recover from a groin injury in time to feature against Norwich City on Saturday.
"Zamora pulled out with an Achilles problem," Jol told reporters following the game. "Johnson has a groin injury. It was in a training session on Saturday. He [Zamora] has had a problem for five or six weeks, so we don’t know [how long he will be sidelined].
"With Andy it is different, hopefully a week. Zamora will not be back for Norwich, as it’s an Achilles injury. Johnson could be. Damien Duff has also had a calf problem for last six or seven weeks, and he pulled out yesterday."
Jol added that he was pleased his change in formation paid off as Fulham recovered from a heavy 5-0 defeat at the hands of Manchester United on Wednesday to draw at Stamford Bridge.
"We played in a different way today, with a 4-3-3 instead of a 4-4-2," he explained. "It was all about how we played. United tried to play around us and they did. We made the decision to play five in midfield as any team in England will have problems against them.
"Sometimes you have to take a gamble and that is what we did today. We had to come up with something else and it paid off. The Manchester United game was very disappointing, but today we showed that against Chelsea we can get a good result."
Andre Villas-Boas' opted to start Fernando Torres in place of Didier Drogba for the clash, with Jol suggesting that the decision may have tactical in order to use the Spaniard's pace.
Jol added: "Every game is different. For us Johnson was injured and Zamora was out. Torres is different from Drogba, maybe they wanted to exploit pace."
The 55-year-old was particularly pleased with the performance of young midfielder Kerim Frei, who was handed his first start for the club.
"I was very pleased with Frei," he said. "He played here in the League Cup and we should have won. In that game he was the best player on the pitch, so I thought maybe he can do it again."
Fulham now turn its attentions to its trip to Carrow Road, and Jol is anticipating a tough test in the form of a confident Norwich side.
"For a team like them it is always good if you’re doing well," he said. "They’re playing with a lot of energy, and especially at home."Follow GOAL.COM USA on