Rennes were denied a stoppage time equaliser by a VAR review as a rarely-utilised rule cost the French club a Europa League point.
Villarreal held on to a 3-2 victory and top spot in Group F, progressing directly to the last 16 of the competition.
While Rennes also go through to the knockout rounds, they will have to negotiate a play-off encounter with one of the teams dropping down from the Champions League if they are to extend their European adventure.
But a home draw would have reversed the two sides’ finishing positions — and it looked like Lorenz Assignon had snatched a point when he rifled home from inside the area in the 11th minute of added time.
It appeared a clean finish from Assignon, who wheeled away in celebration and was soon joined by his teammates, but word of a VAR review was soon relayed to the referee, who paused the restart.
With no offside or possible handballs in the build-up, it was initially unclear what was being checked.
But footage soon revealed the reason for scrutiny.
Assignon’s goal had come shortly after midfielder Enzo Le Fee had struck the bar with a fine free kick. The ball then rebounded back off the woodwork straight out to Le Fee.
A direct free kick cannot be touched by the taker again until another individual has touched the ball. Though Le Fee’s effort hit the crossbar, neither a teammate nor a Villarreal player contacted it before he re-took possession.
The Spanish side were, then, correctly awarded an indirect free kick at the spot at which Le Fee touched the ball by the referee after consultation with the video assistant, and held on for a 3-2 victory.
“I knew the rule existed for penalties, I didn’t know it existed for free kicks,” said Rennes manager Julien Stephan.