Flood, who is also Harrington's brother-in-law, was suffering from food poisoning before the round and eventually had to call it quits on the sixth hole of Durban Country Club.
He was taken to the clubhouse to be treated by a doctor and is expected to be fit to resume his duties on Saturday, although stand-in Pat Cashman has offered his services if required.
Cashman, 65, is a photographer for the Golfing Union of Ireland who has known Harrington for 35 years and was in the gallery following his fellow Irishman while in South Africa on holiday.
Three-time major winner Harrington, who carded a second consecutive 71 to finish two under par, said: "Ronan felt like he needed to throw up and as he went out on the course he thought it would clear a bit but it got worse and worse and for him to give up....I don't think I have ever seen him do that in any circumstances.
"He felt like he was getting in the way and when we finally said goodbye he could not physically stand up. I really did feel bad because he was lying there but thankfully there was a friend of ours out there who holidays down here and he took over.
"He started off like he was carrying bows and arrows but by the end he had the double-strap going (on the bag) and was using all the lingo.
"It's amazing how much caddies do for you and it gives you a new appreciation for what they do out there. I know now why we pay them the big bucks!"
Cashman, who has never caddied before but is a member with Flood at the Heritage in Ireland, said: "The bag was lighter than I expected. It was very comfortable.
"I saw Ronan on the range and he looked awful. I said if you need help, call me. They sent out a replacement caddie but Padraig asked if I would be happy to continue and I was. I told him I wouldn't give him a line or a club but he was so easy to work for.
"I've given him my phone number if he needs me but hopefully Ronan will be okay."