The top-seeded Russian corralled her 29th career crown and second of the year with a 6-4, 6-3 decision over China's Li.
Sharapova, appearing in her third straight final, also claimed the championship at Indian Wells last month.
The Russian star became the first repeat champion in Stuttgart since Lindsay Davenport pulled off the feat in 2004-05.
Li, meanwhile, was playing in her third final of the year. She had earlier won at Shenzhen and fell to Victoria Azarenka in the Australian Open title match.