In what was an emotional fixture for the visitors, Ademola Lookman put his side in front by slotting the ball under Kasper Schmeichel before holding up a shirt in memory of Papa Bouba Diop.
A clumsy Christian Fuchs challenge handed the Cottagers a penalty which Ivan Cavaleiro emphatically converted to double the advantage.
Harvey Barnes lashed home late on to halve the deficit but it was too little to late for his side who slump to their second successive league game.
First half to forget for Fofana
After such a promising start to life in a Leicester shirt, Wesley Fofana endured his most difficult half of Premier League football.
The young defender had the opportunity to put his side ahead but he spurned his chance. Initially, his reaction to the ball coming off the base of the post towards him was impressive but the execution of the finish was not as he stabbed the ball into the crossbar from close range.
Soon after, the Leicester number three switched off at the back and failed to spot and track the run of Lookman, who got goal side of him to score the opener.
In his fledgling career, every game for Fofana will be a learning curve with this half in particular, teaching him how unforgiving the Premier League can be if you don't take your chances or have full concentration in defence.
Despite losing the game and not gaining any points in the short term, the game has the potential to improve Fofana immensely in the long term as right now, it is all about learning from his mistakes to improve his game as he has shown that he has the raw ability now.
Fulham counter Foxes to perfection
It has become apparent this season that Leicester have struggled against teams who have sat back and hit them on the counter attack, something that Fulham executed perfectly.
The Cottagers showed the perfect mix of sitting off and pressing throughout the match and despite having one of the least effective defences in the league before the game, keeping one of the most potent attacks out until the 86th minute was impressive.
The perfect example of the blend that Fulham showed came when the Foxes had possession deep in their box late in the game. Instead of sitting off completely to protect their two goal lead, they saw the opportunity to press and did so with vigour to win back the ball and get a corner out of it.
The visitors were well worth their victory and if they continue to play in the way that they did, they will have a greater chance of playing at the King Power Stadium in the Premier League next season.
Fatigued Foxes head to Ukraine next
It would be fair to say that the available Leicester squad looks fatigued as a smaller number of players have had to cope with a busy schedule in the midst of an injury crisis and while European football had been a target for the East Midlands side, they have felt the strain that comes with it. That strain is only to be worsened as a trip to Ukraine to face Zorya Luhansk is up next for the Foxes.
The news that Ricardo Pereira, Caglar Soyuncu and Wilfred Ndidi could all return to the first team against the Ukrainian side represents a huge boost to Leicester, who against Fulham looked leggy, especially those who played in the make shift defence.
Despite already qualifying for the knockout stages with a last-gasp equaliser against SC Braga, there is still the top spot of the group to play for, meaning that Leicester will be looking to return to England with that secured.
With this, comes the question of whether the squad will be afforded a rest or whether some players will have to dust themselves off from the Fulham defeat and get straight back out onto the pitch.