Del Potro beat Muller 7-6 (7-4), 7-6 (7-4) to earn a berth in Sunday's championship match against qualifier Grega Zemlja of Slovenia, who upset second-seeded Janko Tipsarevic in the other semifinal match Saturday.
It will be the second consecutive year Del Potro has reached the Erste Bank finals. He lost last year to Jo-Wilfried Tsonga.
Zemlja, who ousted No. 3 seed Tommy Haas earlier in the tournament, kept his hot streak going with a 3-6, 7-6 (7-5), 6-2 victory over Tipsarevic, who lost in the Vienna semifinals for the second year in a row.
The loss could cost Tipsarevic a trip to the ATP World Tour Finals. He began the week ranked ninth in the world and the finals field is limited to the top eight players.