It's the second time in two encounters this year that the Dane has beaten the Indonesian, having also clinched victory at the Thailand Open in January.
The win sets up Axelsen for a potential second Super 1000 title this season, having won the Denmark Open in October.
Axelsen will meet Loh Kean Yew in the final on Sunday (28 November) after the Singaporean beat Ramus Gemke 21-14, 21-7 in the other semi-final.
An, who clinched the Indonesia Masters 2021 title last weekend, confirmed her ticket in the final by edging out Pornpawee Chochuwong, 21-19, 21-19.
Intanon last made a World Tour final when she won the Indonesia Masters in 2020, and had to recover in Bali from a game down to beat India's PV Sindhu in the semi-final, 15-21, 21-9, 21-14.
Olympic gold medallists Greysia Polii and Apriyani Rahayu gave the home crowd something to cheer about when they beat tournament third seeds from Thailand Jongkolphan Kititharakul and Rawinda Prajongjai to clinch a spot in the final. In a match that was just two minutes shy of an hour, the Indonesians triumphed 21-18, 21-14.
They will face Matsuyama Nami and Shida Chiharu in the final after the Japanese pair beat South Korea's Baek Ha Na and Lee Yu Rim in the other semi.
Men's doubles top seed pairing of Marcus Fernaldi Gideon and Kevin Sanjaya Sukamuljo have an opportunity to clinch their third Indonesian Open title, having won the event in 2018 and 2019. The world No. 1 pair beat India's Satwiksairaj Rankireddy and Chirag Shetty in the semis, winning 21-16, 21-18.
The final will feature a repeat of the Indonesia Masters line-up after Japan's Hoki Takuro and Kobayashi Yugo secured their spot in defeating compatriots Koga Akira and Saito Taichi 22-21, 21-14.
The Indonesians will be out to avenge their defeat to the Japanese pair last week.
The mixed doubles semi-finals saw top seeds Dechapol Puavaranukroh and Sapsiree Taerattanachai overcome South Korea's Ko Sung Hyun and Eom Hye Won in an epic battle that lasted an hour and 20 minutes.
The Thai pair won the match 21-17, 18-21, 21-14, and will have a chance to win their second title in as many weekends on Sunday.