The world No 11 and European No 2 was forced to withdraw from last week's Nedbank Golf Challenge suffering from a flu virus and food poisoning.
The illness cost him the chance to finish the year in the world's top 10 and up to $1m in prize money.
Chasing the Race to Dubai title took its toll on McIlroy, who flew to China from the emirate to partner Graeme McDowell in the World Cup.
He was second in both and discovered that the playing eight events in the space of ten weeks was just too much for his body.
Updating his blog, McIlroy wrote:
"I think I picked something up on the way from China to South Africa and I was really struggling all week. I didn’t have much energy at all and I think it was a flu virus and with that I got really dehydrated and with the heat at Sun City it certainly made things very difficult indeed. The straw that broke the camel’s back was getting food poisoning on the Friday night! I really wanted to do well in the event as it was my last one of the season so I was really fed up.
"Anyway I was really glad to get home after playing eight out of nine weeks and I’ll know for next year not to do that again – I was really tired and run down and I guess it’s easier to pick up bugs and stuff when the body is in that state – so that is most certainly a lesson learned.
McIlroy took up full membership of the PGA Tour for 2010 and faces a punishing year with several transatlantic trips.
No doubt, his recent experience will stand to him.