In the first set, Axelsen was ahead only once with the score at 2-1. From there on, Gunawan controlled the set and managed to extend the lead, so Axelsen surprisingly ended up losing by ten points.
Axelsen atoned for his poor start from the start of the second set where Gunawan only managed to hold on to 1-1.
The Danish world number four built up a whopping 15-5 lead, before Gunawan managed to get a few points on the scoreboard.
Consequently the match had to be decided in a third set, where Axelsen continued to dominate and completed the comeback while Gunawan was only able to score ni points.
In Saturday's semi-final, Axelsen will meet Frenchman Toma Junior Popov, who is number 18 in the world.
In the women's tournament Mia Blichfeldt is through to the women's singles semi-finals after a two-set win over Rakshitha Sree Santhosh Ramraj.