Wawrinka, in the best form of his life, needed just 65 minutes to win the one-sided final at the Ariake Colosseum, the venue that will stage the tennis competition at the 2020 Tokyo Olympics.
The final was played with the roof closed because of the threat of rain and Wawrinka quickly gained control. He wrapped up the opening set after just 26 minutes with three service breaks.
The second set was much tighter, Wawrinka had to fight off two break points in the third game but he seized his only opportunity, in the 10th game, to complete a straight-sets win.
"I feel great, it's been a really good week for me to win a title again, something always special," said Wawrinka.
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"You don't win a title every week. It's always difficult when I play a good friend like Benoit. I knew before the match he was struggling a bit physically, but I saw the doctor who told me Benoit was ready to play.
"I played my best game today. I felt the ball well and was aggressive. I am very happy to have the trophy tonight."
The win gave Wawrinka his 11th career title, the majority of which have come since he won the 2014 Australian Open. His win in Japan was the 30-year-old's fourth this year after he won in Chennai and Rotterdam and at the French Open.
Paire was appearing in just his fourth ATP career final and his second this year after winning the Swedish Open in July.
The Frenchman, who played Sunday's final with his left ankle heavily strapped, upset Japan's Kei Nishikori in the semi-finals but was no match for Wawrinka.
"It was not easy, when I woke up this morning I could not walk. I was not sure if I could play today," said Paire.
"One hour before the match it was very painful, so I asked: 'What can we do?' I spoke with the doctor and physiotherapist and we made something for my foot.
"I couldn't feel anything in my foot, but I tried to do all I could to play the match and win. It's harsh, but I could not defend on points. Stan played a very good match and congratulations to him. It's back luck for me."
(Reporting by Julian Linden in Singapore; editing by Amlan Chakraborty)
