The pair's participation was threatened after Waterfield went down with flu-like symptoms after arriving from the GB training camp in Xian.
Waterfield, who won synchro silver at the 2004 Olympics with Leon Taylor, admitted he felt he would have to withdraw before improving sufficiently to train on Saturday with Daley for the first time in more than a week.
However, the 30-year-old was still suffering side-effects including having no hearing in one ear and the pair were clearly affected on a windy afternoon at the Oriental Sports Center.
The pair could not maintain a good start and finished in sixth with 407.46points, one place lower and 17.01pts adrift of their efforts in the prelims. The duo, though, were rational.
Daley said: "I thought our performance went okay considering the situation. I think we were very lucky to be able to compete and we did quite well considering the circumstances.
"You have to prepare. It's a 'what if' situation, you have to think of all the things that could happen. It could have happened just before the Olympics and you have to make the most of the situation and we just tried our best after minimal training."
Waterfield concurred, saying: "When you miss a week's worth of training you can definitely tell. I was feeling a little bit flat, I still can't hear out of one ear and mixed in with a bit of wind it's tough.
"The main thing is that when I haven't trained for a week my confidence isn't quite there. So I am a little bit wary, I'm not sure if I'm in the right place.
"When that comes back we will be fine. But I got there and did the best I could."