It had been 15 years since Fulham played at this stage of the League Cup and they came up against a resilient Wycombe side looking to secure their first win in the first round since 2011.
However, with 20 minutes left the Sky Bet Championship side eventually found a way through as Kacaniklic raced on to a Ben Pringle pass to smash home the winner.
Neither side managed to dominate the early proceedings but both had chances, with the hosts going close after Garry Thompson blazed over following neat headed build-up play by Anthony Stewart.
At the other end Kacaniklic found Ross McCormack in space and the Scot fired into the top-right corner only for the offside flag to cut short his celebrations.
The second half also saw few opportunities, but it was Fulham who took advantage of theirs 20 minutes from time.
Pringle ran down the left on the break before sliding the ball back to the penalty spot for Kacaniklic, who smashed home in front of the delirious Fulham fans.