A day of surprises began with defending champion Federer pulling out prior to his semi-final against Jo-Wilfried Tsonga due to a sore back.
The world number three played through the pain during his previous two matches but decided not to risk worsening the problem further ahead of the Australian Open, which starts on January 16.
"I hurt my back in the second-round match (on Wednesday)," Federer said.
"I don't think it's the right time to risk anything right now. For Australia, I'm optimistic. It's not good, but it isn't crazy bad.
"Without playing and the right treatment I will get through it in the next few days. I have a long journey in front of me, but hopefully mid-next week I should be 100 per cent again."
Federer started the tournament in imperious form, dropping just nine games in his opening two matches.
But he struggled in his quarter-final against Andreas Seppi, labouring to a 6-3 5-7 6-4 win.
Tsonga will now meet Gael Monfils in the final after he upset top-seeded Nadal.
Monfils posted a 6-3 6-4 victory in Doha, Nadal's hopes of a comeback thwarted after he had opened a 3-0 lead in the second set.