Ligue 1 side Guingamp were favourites to defeat the second-tier side in Tuesday's contest at Stade de l'Abbe Deschamps and book a return to the Stade de France.
However, Jean-Luc Vannuchi's men deservedly took the lead through Sammaritano's close-range effort in the 15th minute.
Auxerre were forced to play out the final 17 minutes with a man less when Jamel Ait-Ben-Idir was dismissed for a second bookable offence, but they held firm to reach the final where they play either Paris Saint-Germain or Saint-Etienne.
Auxerre came out of the blocks strongly and Gregory Berthier forced Mamadou Samassa into a smart save from the edge of the penalty area.
The hosts were let off the hook when goalkeeper Donovan Leon was caught dawdling in possession by Christophe Mandanne, but the forward was unable to react quick enough to retrieve the ball.
Having survived the scare, Auxerre deservedly took the lead on the quarter-hour mark.
Cheick Diarra's low cross from the left was collected by Sammaritano, who turned neatly on to his left foot and drilled his shot low into the far corner.
Both goalkeepers played their part in keeping the scores at 1-0 in a frantic exchange in the 53rd minute.
First Leon flung himself low to the left to palm out Mandanne's close-range effort, and from the resulting Auxerre breakaway Diarra left Jeremy Sorbon in a twist but saw his dinked effort saved by Samassa.
Ait-Ben-Idir was applauded off despite his second yellow for a late challenge on Reynald Lemaitre, ensuring a nervy ending for Auxerre.
Guingamp pushed hard for an equaliser as the clock wound down and Thibault Giresse was denied by some excellent last-ditch defending by Karim Djellabi.
There was a slight delay in injury time as a section of home supporters prematurely ran on to the pitch to celebrate, but Auxerre bravely held out to pick up a famous win.
