The 18-year-old Scheder picked up silver in the Uneven Bars and bronze in the Balance Beam.
The 21-year-old Seitz, who competed at the 2012 Olympic Games and won All-Around silver at the 2011 European Championships, won silver in the Floor and bronze in the Uneven Bars.
Seitz and Scheder were both included in Germany's team for the Baku 2015 European Games.
The duo were not, however, the only Germans to capture medals in Sao Paulo.
Lukas Dauser won the men's Parallel Bars gold while Leah Griesser collected the women's Floor bronze behind Seitz. And Mathias Fahrig claimed Vault silver and Floor bronze.
The full German Artistic Gymnastics team for Baku 2015 will include Fabian Hambüchen, Sebastian Krimmer, Andreas Toba, Kim Janas, Scheder and Seitz.
Germany was one of four European countries to send athletes to the Sao Paulo World Challenge Cup with Finland, Latvia and Portugal being the others.
The World Challenge Cup was dominated by Chinese and Brazilian gymnasts who collected eight of the 10 available golds 16 of the 30 medals at stake.
The 2015 World Cup and World Challenge Cup season for individual apparatus continues on 7-9 May in Varna, Bulgaria.