The Eredivisie outfit announced on Thursday that the club's record signing had been left out of the 25-man squad due to an "administrative error".
Haller was not on the list of squad changes made for the latter stages of the competition, with boss Erik Ten Hag describing the issue as "unbelievably annoying".
Ten Hag said at a press conference on Thursday: "It's an administrative error. He has not been forgotten. It is indeed a thing with computers: turning a check mark on and off. Something went wrong there. He was definitely on the list."
The 26-year-old joined the Dutch giants from West Ham in a reported £20.2million deal last month.
But Ajax confirmed his inclusion with a statement on the club's Twitter account on Friday, it read: "UEFA has informed Ajax that Sebastien Haller will definitely be available for the rest of the 2020/2021 season in the UEFA Europa League."
Ajax suffered a blow as goalkeeper Andre Onana was banned for 12 months by UEFA's disciplinary body for a doping violation.
Onana had furosemide in his urine following an out of competition test on October 30 last year. The 24-year-old Cameroon international is believed to have mistakenly taken his wife's medication when feeling unwell on the morning of the check.
In a statement on Ajax's official website, the club said UEFA acknowledged that Onana "had no intention of cheating" while managing director Edwin Van Der Sar added it was not a performance-enhancing.
Van Der Sar said: "This is a terrible setback, for Andre himself but certainly also for us as a club. We had hoped for a conditional suspension or for a suspension much shorter than these twelve months, because it was arguably not intended to strengthen his body and thus improve his performance."
The suspension is effective immediately from all football-related activity, with Onana and Ajax set to appeal the decision to the Court of Arbitration for Sport.