Sion knocked Celtic out of the competition with a 3-1 aggregate victory, but were charged by UEFA for using five ineligible players in the two-legged play-off tie against the Scottish team.
A Celtic spokesperson said on Friday: "We have been advised by UEFA that the two protests relating to the matches against FC Sion have been upheld, as a result of which each match has been forfeited in favour of Celtic.
"We are pleased by this decision, the approach which has been taken by UEFA and the fact that UEFA rules and regulations have been upheld. We are also grateful for the support of the SFA in this matter."
UEFA ruled that Sion's Pascal Feindouno, Gabri, Mario Mutsch, Jose Goncalves and Billy Ketkeophomphone all took the field against Neil Lennon's men even though they were not eligible to play.
The five players were not allowed to play as they were signed with the club still under a transfer ban imposed by FIFA after breaching rules over the signing of Egypt goalkeeper Essam El-Hadary three years ago.
Feindouno scored two goals in the 3-1 second-leg win in Switzerland.
Sion were initially drawn against Atletico Madrid, Udinese and Rennes in the group stage of the Europa League, but UEFA have now told Celtic they will take the Swiss side's place in the competition.
"The Scottish club questioned the eligibility of a number of the Sion players who participated in these matches, with the Swiss side winning 3-1 on aggregate," read a statement on UEFA's website.
"The Control and Disciplinary Body accepted both protests and decided to award both ties to Celtic by forfeit (3-0).
"As a consequence, Celtic are qualified for the UEFA Europa League group stage.
"An appeal can be lodged against these decisions within three days of receipt of the written grounds for the decisions.
Sion president Christian Constantin told Swiss television on Friday that he intends to appeal the decision "in both the civil courts and the Court of Arbitration for Sport (CAS)".