I don't think Djoker's fatigue is going to be a big factor. He was faking during the match, stretching and making weird faces when he was down. Once he came back, all of a sudden his pains were gone.
Nadal has also had a difficult week, playing a 2h30m match in the 2nd round with a fever, he might be more rested now, but I would not dare to say he's at 100%. He's been kind of sluggish during the week.
Apart from that, If Nadal loses tomorrow I don't think it's a big deal, he's having a fastastic clay season so far (you cannot expect him to sweep the clay season every single year).
Points earned on clay by Nadal and Djokovic if Nadal loses tomorrow:
Nadal: 1000 + 500 + 600 + 600 = 2700 points.
Djokovic: 250 + 1000 + 1000 = 2250 points.
Djokovic would have one more M1000, but Nadal would have more points overall, so RG is going to be the judge concerning the clay kingdom.