The stadium announcer had already confirmed the goal and Porto had finished celebrating and were back on the halfway line ready for the re-start before Mark Clattenburg, after a long consultation with his linesman, ruled it out.
The incident in Wednesday's 1-1 draw was curious because nobody seemed to notice that the two officials were talking as Porto celebrated.
Television replays suggested that two Porto players were offside when Casemiro snapped up a rebound after Basel goalkeeper Tomas Vaclik had parried Maicon's first effort.
"I have never experienced this, that the assistant has so much courage in bringing a mistake to the referee's attention," said Vaclik. "I was clearly impeded.
"The referee deserves respect for giving us back the goal. I take my hat off to him," added Fabian Frei.
However, Porto coach Julen Lopetegui was less impressed.
"It was a very strange decision and it emotionally affected the team," he said. "It was difficult for us to get going again when the decision was changed after such a long time, and our players reacted very well.
"Can a referee take two or three minutes to make a decision? Obviously, yes, because that's what happened."
The match report on Porto's official website described the delay as "ridiculous."
"The decision was questionable, the delay was ridiculous and it can lead to all sorts of speculation, given that the team of five referees can communicate by radio," it said.
Football's authorities have said that referees can take their time to make decisions, although it inevitably leads to confusion and interrupts the flow of the game, one of the main arguments against the use of video replays.
Last year, Italy's World Cup referee Nicola Rizzoli took around five minutes to make a decision during a league match involving Sassuolo and Roma.
He initially awarded a penalty to Sassuolo, who had put the ball on the spot and were preparing to take the kick when he changed his mind after consulting with his linesman.
FIFA's head of refereeing Massimo Busacca last year said the priority for referees was to make the right decision.
"Sometimes it takes time, two or three minutes, but the important thing for us is the decision which should be correct," he said. "What would be better, to decide in 30 seconds, and give a wrong penalty, or two or three minutes?"
"Everyone says we should use videos but if we have a video, we will waste three or four minutes with every decision."
(Editing by Sudipto Ganguly)
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