Local favourite Kei Nishikori became the first Japanese player to reach the final of the $1.28 million Tokyo event after thrashing Cypriot Marcos Baghdatis 6-2 6-2 in just 61 minutes.
US Open champion Murray's temper erupted on several occasions, the Olympic champion smashing another racquet and yelling furiously at himself after blowing a 4-1 third set lead and two match points.
"He started the match well and I was slow to get off the mark," the world number three said. "There was always going to be a bit of residue from the last few months."
Murray was broken by the Canadian in the first game and a booming forehand by Raonic on his first set point forced the top seed into a shanked backhand which flew high into the crowd.
The Scot faced break points in the second set and angrily trashed his racquet for the second match in a row as sixth seed Raonic continued to blast winners past him.
But Murray, who also reached this year's Wimbledon final, dug in to win the tiebreak 7-5 with a fizzing backhand return onto the laces of Raonic on his first bite at the cherry.
Raonic, who has been taking rickshaw rides around ancient Tokyo and shown a keen interest in samurai swords, twice gifted Murray match points with double-faults at 5-6 in the decider.
Both times his serve bailed him out.
"He played well behind his first serve," said Murray, who had thrashed Raonic 6-4 6-4 6-2 in the fourth round of the US Open last month. "That made it tough for me."
Raonic, dressed like a throwback with 1970s-style striped shirt and headband, clinched victory with another vicious serve Murray could only slam long after two hours, 46 minutes.
"I wasn't being aggressive at the US Open," said Raonic, who fired down 13 aces and won 82 percent of points on his first serve.
"From the first match here I tried to play under my terms and turned it around."
Raonic, who also saved a match point in his quarter-final victory over Serbia's Janko Tipsarevic, promised to take care of business against eighth seed Nishikori.
"Nishikori is having a good week and is capable of great things," said the 21-year-old, chasing his third title of the year.
"If I play on my terms and under control, then I think it will be in my hands."
Nishikori could be a handful in front of a Japanese crowd.
"It's hard to believe I'm in the final," said the world number 17, who knocked out second seed Tomas Berdych in the last round.
"Last night I played at over 100 percent. Today I was at 80 or 90. I've always struggled to play well in Japan with all the pressure. It's a dream to be in the final."
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- Kei Nishikori