The 24-year-old went down clutching her knee in the second half of the Gunners' 3-2 loss at the Emirates, which sent Wolfsburg through to the final 5-4 on aggregate.
Wienroither was named on the bench by Jonas Eidevall, who opted to start Noelle Maritz on the right-hand side, but the Austrian was introduced just after the hour mark with Arsenal 2-1 down.
However, Wienroither had to be stretchered off just 18 minutes later after a nasty-looking fall, and she emerged on crutches to console her teammates at the full-time whistle.
Wienroither's knee noticeably jolted just before she hit the turf, sparking immediate concern about another potentially serious injury for Eidevall's side, who are already without Beth Mead, Vivianne Miedema and Leah Williamson due to ACL ruptures.
The Gunners released a medical update on Thursday morning confirming that Wienroither's issue was as serious as first feared, and she will miss the rest of the season as she prepares to undergo surgery.
"We can confirm that Laura Wienroither suffered a ruptured anterior cruciate ligament in our match against Wolfsburg at Emirates Stadium on Monday evening," the update read.
"Laura was substituted in the 82nd minute of our UEFA Women's Champions League semi-final and has subsequently undergone testing to determine the extent of the injury.
"Laura will undergo surgery in due course and will be sidelined for an extended period. Everyone at the club will now be supporting Laura and working hard to support her recovery and return to action."
Wienroither, who joined Arsenal from Hoffenheim in January 2022, ends her first full season at Arsenal with one goal from 28 matches in all competitions, coming off the bench in March's League Cup final win over Chelsea.
The Austria international joins fellow ACL victims Williamson, Mead and Miedema on the sidelines amid growing calls for more research to be done on the prevalence of such serious issues in women's football.
Williamson and Miedema are already confirmed to be missing this summer's World Cup, while England boss Sarina Wiegman has admitted that Mead will need a "miracle" to recover in time for the tournament.
Arsenal also lost captain Kim Little to a season-ending hamstring injury last month, while Australian forward Caitlin Foord was unavailable for the defeat to Wolfsburg in North London due to her own hamstring issue.
Eidevall's side sit fourth in the Women's Super League table with 38 points from 17 matches - nine adrift of leaders Manchester United with two games in hand - and they return to action against Leicester City on Friday evening.