Baghdatis will face Olivier Rochus in the final after the Belgian outlasted rising Brazilian Thomaz Bellucci 7-6, 4-6, 6-3.
Soderling, the top seed, was unable to play because of an elbow injury.
"I've been struggling with this injury for three months, really," Soderling told Swedish public television SVT.
The world number 10, who is chasing a spot in the season-ending Masters Cup in London, received treatment for the injury during his quarter-final win over Spaniard Guillermo Garcia-Lopez.
"Sometimes, it's been better, sometimes worse. This week it hasn't been good at all and I've really had to fight my way through the matches. Yesterday, against Garcia-Lopez it was really, really bad and it was not any better this morning."
Soderling lost in the Stockholm final last year to Argentine David Nalbandian.
"We're at the end of the season and there are two big tournaments left. I'm going to have to do well at them if I want to reach the Masters.
"I won't be able to do that, if it continues to feel this way. Hopefully, it will be little better in one week or two, so that I'll be fit at least for (Masters Series event) Paris," added the French Open finalist.
Paes-Dlouhy advance at Halle
Argentina name Del Potro for singles
Nalbandian has hip surgery, could miss four months
Federer-Wawrinka seal tie for Swiss
Top seed Soderling cruises in Stockholm