Momota will play Axelsen's fellow Dane Rasmus Gemke, who is unseeded, in the last four on Saturday.
Victory for the all-action Momota, the reigning two-time world champion, was his 13th in 15 matches against Axelsen, now ranked sixth in the world.
"I'm getting closer and closer," the 25-year-old Axelsen, whose career has recently been disrupted by injury, said after forcing Momota to three games.