Al Ahly of Egypt defeated CS Sfaxien of Tunisia in the final to win their fifth title and for the second time in a row with a late winner by Mohamed Aboutrika.

AlAhly keep the trophy forever after 3 cups 1 The tie between AS Port-Louis 2000 and Coin Nord was played over one leg only by mutual consent.

1 The match was abandoned at 9' of injury time in the first half with Hearts of Oak leading 2–0, after Saint-George SA walked off protesting the officiating.

2 CAPS United were ejected from the competition after 1st leg, when it was discovered that false information had been submitted for two Malawian players in their first round match against AS Inter Star.

The top scorers from the 2006 CAF Champions League are as follows: