Allen, who finished fifth in the Rio Olympics in the 110-meter hurdles, suffered the torn ACL covering a punt in the fourth quarter.
He has four receptions for 141 yards and one touchdown this season.
Allen had returned to Eugene several practices into fall camp in order to compete with the football team this fall.
Allen had been a key part of the Ducks receiver depth already this season, catching four passes for 141 yards and one touchdown. His top end sprinting speed have the Oregon offense an opportunity to lengthen the field in the pass game.
The season-ending injury is the second of Allen's football career. He suffered a torn ACL in the Ducks' 59-20 win over Florida State in the 2014 Rose Bowl. He rehabbed that injury to return for the 2016 Oregon track season, which led into his Olympic bid.
Allen is the 2014 and 2016 NCAA champion in the 110-meter hurdles, as well as the 2014 USATF 110-meter hurdle champ.
Information from ESPN's Chantel Jennings was used in this report.