Fulham started well and were rewarded when Alexander Kacaniklic fired them into the lead before two late goals from Dimitar Berbatov and Urby Emanuelson meant they left South Wales with all three points.
Speaking to Sky Sports after the match, Jol said his side deserved the win, which saw Fulham finish 12th in the table.
Jol said: "The first half we were disciplined and in the end it was an ugly win.
"We have 43 points to end the season and the only difference between us and Swansea was that they beat us in the home fixture.
"It's a fantastic day for us and the club and now we have to plan for next season."
Several of Fulham's players are at the club on loan and Jol says that there will be changes, adding: "Five or six players will be going back to their clubs. We, in the future, want to start winning in a good way so we will have to bring two or three in.
"In midfield today we had shape and I thought Frimpong performed like a real warrior.
"At the moment Mark Schwarzer's future is unclear but we are hopeful of sorting something out over the next few weeks."