Del Potro, who lost to Jo-Wilfried Tsonga in the decider 12 months ago, edged two tie-breaks to win 7-6 (7/4) 7-6 (7/5) and earn valuable points in the race to qualify for the Barclays ATP World Tour Finals.
Janko Tipsarevic's hopes of making it to London were hit, though, as he was upset 3-6 7-6 (7/5) 6-2 by Slovenian qualifier Grega Zemlja.
It was the first time the world number 70 had beaten a top-10 player and sent him through to a first ATP World Tour final.
Zemlja revealed he almost did not play in Vienna, saying on www.atpworldtour.com: "It was an interesting and difficult situation for me before the tournament.
"I was preparing last week for this tournament and I found out I was the first on the waiting list to get into the main draw in Stockholm.
"So I was deciding whether to go to Stockholm or play in the qualification here. I said I'd rather play here and that I have a good feeling. I think it was a pretty good decision."