Substitute Clarck N'Sikulu and Modou Sougou secured a famous victory and ended the Ligue 1 champion's long unbeaten run in Annecy.
The last time the defending champion avoided defeat for so long was during the title-winning season of 1993-94, while PSG came into this encounter without a defeat in 90 minutes in 36 matches in all competitions.
Both sides missed several chances in the first half and it remained goalless until the 75th minute when substitute Clarck N'Sikulu hit a controlled shot into the bottom corner.
Javier Pastore went close to leveling with three minutes left, but goalkeeper Jesper Hansen made the save before Modou Sougou completed a famous home win.
PSG pressed with intent in the final 10 minutes, but poor distribution coupled with Evian's determined defending ensured that the home side took all three points.