Nadal had been a clear favourite to face Djokovic in Sunday's showpiece at Caja Magica but the 17-time Grand Slam champion extended his stuttering build-up to the French Open with another surprise defeat.
It was also Djokovic third title in Madrid (he's 3-0 in finals) and 74th overall, first since Melbourne. His straight set win over a stellar clay court player in Dominic Thiem during the semifinals was unbelievable. They make you suffer, that's all they do.
Nishikori's compatriot and world number one Naomi Osaka is through to the quarter-finals of the women's tournament for the first time after she eased past Belarusian Aliaksandra Sasnovich 6-2, 6-3.
Nadal, still seeking his first title of the season, had also failed to make it to the final in Monte Carlo and Barcelona, tournaments he had won the last three consecutive seasons.
After starting slowly on clay last month after another knee injury, Nadal is hopeful of quick progress, but he has alluded to the fact that he could walk away if he cannot return to his best.
Nadal said it was impossible to know what the current setbacks could mean for his future.
Djokovic, who won in Madrid in 2011 and 2016, had played only four sets in the Spanish capital this week ahead of the semifinals. That was his first tournament victory since the Australian Open. For sure, it's part of the plan at some point to get physically better, do everything better, be more professional and avoid that kind of things because, as you have seen, Djokovic and Nadal have been doing well in tournaments over and over and over again, week-by-week. It was three [losses to Nadal] in a row ... He's played in four French Open finals since 2012.
"I was still kind of trying to find my best game on clay", Djokovic said.
"I've won a lot over the years on this surface", he said".
"In Paris, I have 11 titles". Along came Nadal, and all that sharing of the wealth was brought to a crashing halt.
"He deserved the victory, he played unbelievably". Moreover, this year Novak didn't start his season with a winning momentum as in Qatar Open 2019 he was shocked by Roberto Bautista Agut in the semifinals which was later followed by one more defeat against Philipp Kohlschreiber in straight sets at Indian Wells 2019.
We don't think so.
By his own high standards, Nadal's clay-court swing has been disappointing.