Schalke, last season's Cup winners, won 4-3 on penalties after a goalless draw against their old enemies Dortmund, the Bundesliga champions.
Fahrmann spent several seasons at Schalke as a youngster but left in 2009 after finding his progress blocked by Neuer who has established himself as one of Europe's top goalkeepers.
The 22-year-old moved to Eintracht Frankfurt but returned to Gelsenkirchen in the summer after Neuer's move to Bayern Munich.
Dortmund made most of the running in the first half and Fahrmann produced a superb one-handed save to deny Robert Lewandowski before half-time.
The second half was more even and Fahrmann's opposite number Roman Weidenfeller brilliantly diverted Jan Moravek's finish wide when the Czech looked certain to score.
Fahrmann ensured Schalke's win by saving penalties from Kevin Grosskreutz and Ivan Perisic.
The Super Cup was officially reinstated by the German federation last year after a 14-year absence.
The Bundesliga starts in a fortnight's time with the first round of the German Cup next weekend.
