Nishikori hopes to make the final of the prestigious season-ending event for the first time after reaching the last four in 2014.
Nishikori was denied a second Grand Slam final appearance in September when Wawrinka defeated him in the US Open semi-finals and the world number five got his own back with a dominant display at London's O2 Arena.
Despite being placed in a tricky Tour Finals group that also includes world number one Andy Murray and former US Open champion Marin Cilic, Nishikori hopes to make the final of the prestigious season-ending event for the first time after reaching the last four in 2014.
"I was very solid from the first game and very confident. It wasn't easy against Stan because he hits a lot of slice and a variety of shots, but I played a good game today," Nishikori said.
Florida-based Nishikori also harbours hopes of overhauling Wawrinka in the race to finish the year in third place in the ATP rankings and this victory keeps him on course.
"That is my goal for this week, to win matches and reach number three. I see the opportunity to go up the rankings and I've been playing well so I hope to keep it up," Nishikori said.
Wawrinka had reached the semi-finals of the Tour Finals for the last three years and held a 4-2 lead in his career head to head with Nishikori.
But he was no match for the 26-year-old, who was fired up to make amends for his loss in New York, where he reached his only major final in 2014.
After a tight start, Nishikori seized the momentum in the fifth game, punishing some sloppy play from Wawrinka to earn two break points and converting the second with a fizzing forehand that the Swiss star couldn't handle.
Nishikori pressed home his advantage with another break for a 5-2 lead before serving out the set with the minimum fuss.
Wawrinka had come from a set down to beat Nishikori in their US Open clash but, with a strapping on a left knee injury that has troubled him recently, the 31-year-old was looking tentative this time.
Aided by Wawrinka's growing number of unforced errors, Nishikori broke again in the fifth game of the second set when the world number three allowed a return of serve to drift past him and bounce in.
Nishikori needed little encouragement to seal the win and turned the screw to induce one more decisive break.