The usually biting BBC programme remembered its sometime presenter and panellist by showing clips of his early and latest appearances.
As guest host Jack Dee read out the final scores, he told viewers: “Of course the scores have always been hotly contested on this show.
“Here’s a friend of the show who always had the right attitude even when he hadn’t won.”
The programme then cut to a vintage clip of a fresh-faced Mr Kennedy joking about how the Liberal Democrats were causing a shift in politics and admitting he would have been “very happy” to come second in an election.
In a second, more recent clip Mr Kennedy traded barbed quips with former Top Gear presenter Jeremy Clarkson after being asked about Government plans to imprison bankers.
Kennedy replied: “It’s a bit stupid for David Cameron to suggest this, he hasn’t got anywhere to put them for a start and probably most of them are voting Tory, aren’t they Jeremy?”
After Clarkson replied that he could not understand Scottish, Mr Kennedy said: “Don’t worry Jeremy, most people in Scotland can’t understand voting Tory either.”
Fans of the show praised the homage for showing Mr Kennedy’s humanity and humour.
Jamie Shoesmith tweeted: “Wonderful tribute to Charles Kennedy on Have I Got News For You, showing his excellent funny side. Rare moments for any politician who appeared on the show.”
Kathy Hurst said: “Liked that Have I Got News For You tribute to Charles Kennedy then. Not fawning - showing the humour and brilliance of the man.”
Ben Dowell tweeted: “Good on Have I Got News For You for Charles Kennedy tribute at the end. He put Clarkson in his place.”
The results of a post-mortem examination released yesterday revealed that Mr Kennedy had suffered a “major haemorrhage” as the result of his long fight with a drinking problem.