Siegemund, who had beaten top-10 players Agnieszka Radwanska, Roberta Vinci and Simona Halep in her previous rounds, raced to a 3-0 lead in the first set, frustrating the Australian Open champion with repeated drop shots.
Kerber, however, quickly reined in her fellow German, breaking the 28-year-old three times to clinch the first set 6-4.
Siegemund, the world number 71 who had never reached a WTA Tour final in her 10-year professional career, needed treatment for a back injury early in the second set.
She came back only to see Kerber inflict further damage with her trademark forehand down the line to go 5-0 up.
The left-handed Kerber then wrapped up the win when Siegemund sent a slice backhand into the net.
"It could not get any better here than today," said Kerber.
"In the first set I needed to find my rhythm in the beginning. She played a great tournament and I am happy I could beat her today. It was special to win here again."
After a demanding week, Siegemund felt her fitness was lacking in the second set.
"At the moment I am disappointed," she said.
"I am completely empty today. I could have played better but she did well. But I had a good week. I reached my limits. At such a level you need the fitness and after seven matches I was missing that today."
(Reporting by Karolos Grohmann; Editing by Toby Davis)
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