Twenty-four hours before their final group game against the French club on December 9, Spurs decided the match could not go ahead after eight players and five members of staff tested positive for Covid-19.
Rennes, who had already travelled to London, accused Spurs of making a "unilateral decision" and a “lack of fair play”.
Spurs were desperate to reschedule but, after talks with both clubs, UEFA revealed the fixture could not go ahead after being unable to find a suitable date before the December 31 deadline.
Spurs proposed playing last Wednesday, if the Premier League would agree to postpone Thursday’s match against Leicester, and even offered to reverse the fixture and play in France.
The League’s board declined but the game was subsequently called off on the day following an outbreak in the Leicester camp.
A 3-0 win for Rennes, who had already topped the group, means Spurs finish third in Group G and crash out of Europe, with Vitesse Arnhem progressing to a play-off against Rapid Vienna to reach the knockouts.
The decision was made by the UEFA Appeals Body, which leaves Spurs with no recourse to appeal through UEFA and the club reluctantly accepted the decision.
A Tottenham spokesperson said: “We are disappointed by the ruling of the UEFA Appeals Body and the refusal to allow more time for the match to be rescheduled.
“We have to accept this ruling, however, and our focus now turns to the competitions we remain in.”
A UEFA statement read: “The Chairman of the UEFA Appeals Body took the following decision: To declare the 2021/22 UEFA Europa Conference League group stage match between Tottenham Hotspur FC and Stade Rennais FC, that was initially scheduled to be played on 9 December 2021, as forfeited by Tottenham Hotspur FC, who is therefore deemed to have lost the match 0-3 in accordance with Annex J.3.1 to the Regulations of the UEFA Europa Conference League (2021/22 Season)."