Philippe Senderos nodded home his first ever Cottagers goal in the 89th minute to ensure the hosts secured a 2-1 win after controversy threatened to alter the course of proceedings.
The officials waved play on having ruled the ball was not fully over but manager Jol says replays show it should have stood.
"I asked Pav and he said 'no, it was not over the line'," the Dutchman said.
"I thought therefore it was not over the line but our video guy showed me it was.
"It was a goal. Maybe what Sky or BBC saw was different but what I saw from my TV man was it was behind the line.
"We were in Geneva with a lot of coaches and we listened to [UEFA president Michel] Platini, who said 'it is a game of human beings'.
"Everyone makes mistakes and when you think how many times it happens in a season, it is four or five times.
"Everybody agreed to leave it like but that was two years ago and there is now endless discussion."