Sale remain in contention for an automatic Heineken Cup spot next season after a hard-fought tussle at Stade Armandie.
The Sharks, without inspirational skipper Jason Robinson because of flu, move into the semi-finals of the European Challenge Cup, despite losing to Agen by two points.
Sale took a 16-point advantage into the second leg of the quarter-final, but needed only three of them in a tight match between two evenly-matched teams.
The Sharks will play Irish province Connacht in a two-leg semi-final, with the eventual Cup winners guaranteed a place at the top table of European rugby next season.
Agen - who are lying mid-table in the Championship with eight victories in 16 matches - scored tries through centre Conrad Stoltz and former Test powerhouse Christian Califano in the first half.
But the visitors stayed in touch with regular goals from Charlie Hodgson.
The incumbent England fly-half banged over four penalty goals as Sale went into the break trailing 17-12 on the scoreboard, but leading by 11 points overall.
Hodgson put his side 14 points clear with his fifth goal, but could not bag the sixth which would have given his side victory.
Agen held on in the dying minutes to record the win, but their involvement in European rugby this season has finished.
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