The double world champion finished equal on 1729 points with Slovenia's Peter Prevc, who finished second on Sunday, but took the overall title after winning nine events this season to Prevc's three.
Norway's Rune Velta finished third in the final event of the winter.
Freund, 26, becomes the third German to win the crystal globe after Martin Schmitt in 1999 and 2000 and Jens Weissflog in 1984.
Planica results (after two jumps):
1. Jurij Tepej (SLO) 436.4 pts (230.5 + 244.0 m), 2. Peter Prevc (SLO) 433.6 (236.5 + 233.5), 3. Rune Velta (NOR) 418.2 (230.5 + 226.5), 4. Stefan Kraft (AUT) 415.7 (229.5 + 229.5), 5. Kamil Stoch (POL) 412.5 (230.5 + 222.5)
Selected: 7. Severin Freund (GER) 409.9 (222.5 + 226.0 m), 8. Noriaki Kasai (JPN) 405.5 (223.5 + 229.0), 9. Gregor Schlierenzauer (AUT) 401.0 (228.5 + 218.0)
Overall World Cup standings (after all 32 events):
1. Severin Freund (GER) 1729 pts (winner), 2. Peter Prevc (SLO) 1729, 3. Stefan Kraft (AUT) 1578, 4. Anders Fannemel (NOR) 1161, 5. Michael Hayboeck (AUT) 1157, 6. Noriaki Kasai (JPN) 1137, 7. Roman Koubelka (CZE) 1113, 8. Rune Velta (NOR) 848, 9. Kamil Stoch (POL) 820, 10. Gregor Schlierenzauer (AUT) 739, 11. Simon Ammann (SUI) 646