As a result, the Cowboys' starting running back is once again in line to serve his six-game suspension, none of which has been served so far.
The court says the appeal will be heard on an expedited appeal.
Elliott and the NFLPA next can appeal to the full appeals court and then to the U.S. Supreme Court, if they choose.
However, the one positive to Thursday's ruling is that he'll now be eligible to return on Christmas Eve in a Week 16 matchup with the Seattle Seahawks and can participate in the postseason if the Cowboys make it.
Elliott and the NFLPA challenged the decision-making process in court, arguing the NFL's investigation was fundamentally unfair to Elliott.
As a rookie last season, the former Buckeyes standout rushed for a league-leading 1,631 yards over the course of 15 regular-season games for the playoff-bound Cowboys. The NFLPA appealed, and the 2nd Circuit granted a temporary stay for Week 9 that let Elliott take the field on Sunday against the Chiefs.
The court's ruling allows the NFL to re-suspend Elliott for six games, per NFL Network's legal analyst Gabe Feldman.
The 2nd U.S. Circuit Court of Appeals reviewed the case after Elliott received an administrative stay in NY federal court last Friday.
Elliott is second in the NFL with 783 rushing yards and tied for the league lead with seven rushing scores.