Axelsen, who beat two-time Olympic champion Lin Dan of China to clinch the world title in Glasgow last month, overpowered South Korea’s Son with a 21-16, 21-16 win.
He now faces Malaysian Lee Chong Wei who has won the Japan Open six times. Lee booked a spot in the final after a 21-19, 21-8 win over China’s Shi Yuqi.
In the women’s singles, Spain’s Carolina Marin, Olympic gold medalist last year, reached the final as Japan’s Nozomi Okuhara dropped out from the semifinals due to knee trouble.
Marin faces China’s He Bingjiao who beat Chen Yufei 21-14, 25-23.
Okuhara, newly crowned women’s world champion, was aiming to reclaim the trophy on home soil after winning it in 2015.
Home fans at the Tokyo Metropolitan Gymnasium expressed disappointment when the organizers announced her withdrawal.
“I did my best (to recover) but this morning, I wasn’t in the condition to play,” Okuhara, 22, told reporters, according to Sankei Sports.
“I was ready for a battle mentally but my body was telling me I couldn’t,” she said in tears.