Wozniacki beat second-seeded Simona Halep, 7-5, 5-7, 6-2, while home favorite Kerber defeated American Madison Brengle, 6-3, 6-1, in less than an hour.
It will be Wozniacki's second final at Stuttgart after she lost in 2011 to Germany's Julia Goerges.
The fourth-seeded Dane needed almost three hours to prevail over Halep, winning four games in a row in the third set to go 5-1 ahead. After missing three match points and being broken while serving for the match, Wozniacki broke the Romanian again to close out the win.
Despite the loss, Halep will move up to No. 2 when the world rankings are updated on Monday, jumping over Maria Sharapova, who lost to Kerber on Thursday.
Kerber has a 5-4 record against Wozniacki, winning in the Stuttgart second round in 2012. Kerber won her fourth WTA in Charleston this month, while Wozniacki won her 23rd in Kuala Lumpur last month.
Defending champion Kei Nishikori is back in the final of the Barcelona Open after beating Martin Klizan of Slovakia, 6-1, 6-2.
Klizan had won their only previous match at last year's French Open, but Nishikori dominated their second meeting on the same outdoor court where he won his first clay-court title.
Nishikori won the first five games of the match and saved all six of Klizan's break points.
The 25-year-old Nishikori is seeking to add to his eight career titles.
Nishikori had another strong start by claiming 21 of the first 27 points with a complete mix of winning shots, including a beautiful lob that fell on the line.
Nishikori closed out the first set with a slicing backhand approach shot and broke Klizan early in the second set to win in 1 hour, 17 minutes.
Andujar hit 32 winners to Ferrer's 19 and finished off the upset with a drop shot that Ferrer couldn't reach. Andujar, ranked 66th, had not taken a set from the eighth-ranked Ferrer in three previous losses.
Guillermo Garcia-Lopez of Spain and Jiri Vesely of the Czech Republic will play for their second ATP title of the year in the Nastase Tiriac Trophy in Bucharest, Romania, where they will meet for the first time on tour.
Sunday's finale was set up when Garcia-Lopez lost his serve only once in beating Gael Monfils of France, 6-7 (2), 6-4, 6-2, and Vesely also staged a comeback to top Daniel Gimeno-Traver of Spain, 2-6, 6-1, 6-4, in the semifinals.
Fifth-seeded Garcia-Lopez won his fourth career ATP title in February at Zagreb. This is his eighth final. Seventh-seeded Vesely won his only previous tour final in January at Auckland.