Spurs were unable to fulfil the December 9 fixture due to a swathe of Covid-19 cases in the squad.
No agreement could then be reached between the clubs for a rearranged date before the deadline of December 31.
As a result Tottenham finish third in the section behind group winners Rennes, who progress directly to the last 16, and Dutch side Vitesse who now face Rapid Vienna in a knockout play-off.
“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,” read the UEFA statement.
The match in London was called off after Spurs manager Antonio Conte announced on the eve of the game eight of his players and five members of staff had tested positive for Covid-19.
Rennes accused Tottenham of creating a “London fog” as the game was postponed shortly after they had landed in the English captial.
According to UEFA rules, a match should be played as long as both teams have 13 fit outfield players and a goalkeeper.
“We are disappointed by the ruling of the UEFA Appeals Body and the refusal to allow more time for the match to be rescheduled,” Tottenham said in a statement.
“We have to accept this ruling, however, and our focus now turns to the competitions we remain in.”
Spurs have been one of the hardest hit English clubs by the resurgence of Covid-19 as case numbers across the country surge due to the emergence of the Omicron variant.
Tottenham’s recent league games against Brighton and Leicester were also postponed.
However, unlike many of their domestic rivals, they returned to action this weekend in a 2-2 draw with Liverpool.