Despite having control of the Carabao Cup first-round tie, it took until the 67th minute for the Cottagers to take the lead they deserved through Lucas Piazon's superb strike.
But this was a satisfying evening for the Championship side, who changed their entire line-up from last Saturday's draw against Norwich, as they won at Adams Park in this competition for the second time in three seasons.
Jokanovic said: "The game was competitive and we played well despite missing a bit of quality in the final passes in the midfield in the first 45 minutes, when we had possession but we didn't score the goal.
"In the second half, we showed our ambition for winning the game and we scored a quality goal and after that we scored the second and killed the game.
"It allowed us to finish the game comfortably, which is something we didn't find in the first game against Norwich.
"I think it will give us big confidence, scoring the second goal, because we missed this situation in our first game and we found it today.
"It's the beginning of the season and this is not our best, I'm sure, right now, but the players need to compete and gain the minutes in the field and I didn't have to make so many substitutions today."
The deadlock was broken when Piazon was given time to line up a shot from 25 yards and his effort flew into the top corner.
The game was made safe with nine minutes left when Piazon's corner was flicked in at the near post by the impressive Denis Odoi.
Wycombe boss Gareth Ainsworth said: "I'm gutted we're out of the cup, as it's always nice to have a cup run, but I thought there were some good performances from the boys.
"There were some good positives for me, I'm just disappointed about conceding from a corner because that's bog-standard.
"In League Two, the Championship, the Premier League, a corner's a corner and you've got to defend the corners right and that's at 1-0, with us scrambling and putting a bit of pressure on at the end.
"But 2-0 is always hard to get back against a team like Fulham because they're just going to keep the ball with no pressure on them and even if they make a mistake it's only 2-1.
"So there are some disappointing bits tonight, but on the whole I'm pleased and with Port Vale playing tomorrow night against Leeds, we get a day more rest which could be important."