French Open champion Wawrinka took just 65 minutes to complete victory in Tokyo with Paire, who underwent a scan on his left ankle before the final and needed pain-killing injections to play, clearly in discomfort.
"It feels really great, it's been a special week," said Wawrinka, sporting a red "Stan the Man" T-shirt and snapping selfies with the silver trophy.
"I took my time to get to the top but once I get somewhere, I stay," added the Lausanne native after winning his 11th career title.
"Once I started to beat the top guys and win trophies, I got the confidence to know I can do it. But four in one year is amazing."
Wawrinka, the top seeded player in the tournament, quickly found his groove and fierce pressure earned him a break for 4-2 in the first set.
The world number four pressed home his advantage with a thumping crosscourt forehand which wrong-footed his close friend Paire.
With little left in the tank after toppling defending champion Kei Nishikori in Saturday's semi-finals, Paire took a tumble early in the second set but gamely battled on despite being obviously in pain.
The "lucky" sneakers held together by tape he wore in his win over Nishikori granted Paire no such mystical powers against Wawrinka as he looked to become the first Swiss to win the Japan Open since Roger Federer in 2006.
Several times Wawrinka's dipping one-handed backhand, one of the most potent weapons in men's tennis, whistled past a grimacing Paire, whose brave resistance finally ended when he coughed up a double-fault on match point.
Wawrinka, who is a perfect 4-0 in finals this year and is one of four players — along with Novak Djokovic, Andy Murray and Federer — already qualified for next month's season-ending ATP Tour Finals in London, confessed to having mixed feelings after his victory.
"I knew before the match Benoit was struggling a little bit physically," said Wawrinka.
"But I played my best tennis. I played very aggressive and kept him on the back foot."
Paire, meanwhile, has pulled out of next week's Shanghai Masters event because of his injury.
"When I woke up today I couldn't walk," said the Frenchman, projected to rise from 32 to around 25 in the world rankings following his fine Tokyo run after finishing an injury-hit 2014 season at 118th.
"An hour before the match I wasn't sure I could play. I had injections in my ankle and just couldn't feel anything.
"It's tough to move when you don't feel your feet," he added.
"But I gave everything I could give. I lost to my best friend so I'm not really sad."
Meanwhile, at the women's China Open in Beijing, Switzerland's Timea Bacsinszky lost in the final to Spain's Garbine Muguruza, 7-5, 6-4.
Bacsinszky's strong performance in the tournament, however, means she will jump into the top ten WTA rankings from 17th.
The tournament marked her fourth final appearance this year, including two wins in Acapulco and Monterrey.