Wawrinka and Nishikori played out another gruelling contest as the temperature and humidity remained brutal for the second semi-final, with the Swiss proving just the stronger.
Nishikori looked sharper for the best part of two sets but was pegged back by Wawrinka with a break at the end of the second.
The Japanese player appeared to be suffering for his four-hour quarter-final win over Andy Murray but he recovered from 4-1 down in the third to level, with play interrupted briefly as rain forced the roof to be closed.
A relieved Wawrinka let out a huge roar when he saved a break point at 4-4 and powered through five straight games to move a break up in the fourth.
There was one final push from Nishikori, who broke back when Wawrinka played a woeful service game at 3-2, but the former French and Australian Open champion reeled off another three games in a row to clinch victory.
"Kei is a tough player and he played well from the beginning," said Wawrinka. "I had to wait and fight and make him a bit uncomfortable and he started to get tired.
"That is when I put my game to be aggressive. To be in the final is something crazy."