The controversial club lost the second leg 1-0 away to second division runners-up Aarau but held out comfortably for a 3-1 aggregate win.
Sion would almost certainly have finished bottom of the table after the penalty but were saved when Neuchatel Xamax were kicked out of the league in January for a series of financial irregularities under Russian-born owner Bulat Chagaev.
Neuchatel officially finished bottom of the 10-team standings, the only direct relegation spot, giving Sion ninth place and the chance of a play-off.
There was still controversy as Aarau protested over the presence of Sion's Serey Die, even though he was handed an eight-match ban two weeks ago for slapping a ball boy in the face.
The Ivorian appealed the decision and, under the competition rules, was allowed to continue playing until the hearing takes place, which might not be until next season.
Sion were kicked out of the Europa League this season for fielding players they had signed while subject to a FIFA transfer ban.
The club's volatile president Christian Constantin then took the case to a civil court, defying FIFA and UEFA statutes, and Switzerland was threatened with an international ban unless action was taken against Sion.
Having lost their case, Sion were deducted 36 points.
The match brought the curtain down on one of the most tumultuous seasons Switzerland has experienced, with crowd violence forcing a Grasshoppers-FC Zurich derby to be abandoned and Servette Geneva also filing for bankruptcy.
