It had been suggested Alli was expressing dissent at referee Clement Turpin and could face retrospective punishment, but the 21-year-old insisted former Spurs team-mate Kyle Walker was the intended subject of the signal as a joke.
Pochettino does not feel it is a "big issue" and praised the development in the midfielder's temperament, which has been the subject of scrutiny since a three-match ban for punching Claudio Yacob in April 2016.
"Dele Alli has improved a lot from last season and his behaviour is fantastic. That was a joke with a team-mate. He was unlucky because the camera caught that moment," said Pochettino.
"I am not worried, I think it was the heat of the media afterwards. It is not a fantastic gesture, I think it's not a big issue, although it was a shock in the moment.
"It was something with his team-mate, no big issue for FIFA or for us. Things happen on the pitch. From my point of view it is not a big issue, he should not be banned by FIFA."
Another player whose behaviour has come into question is new signing Serge Aurier.
The right-back, who arrived from Paris Saint-Germain for a reported £23 million on deadline day, was forced to train with the Ligue 1 club's reserves after making a homophobic slur about former coach Laurent Blanc, while he was convicted for assaulting a police officer last year.
However, Pochettino is willing to give Aurier a clean slate at Spurs.
"I'm the first to make mistakes in my life. It's important people give the opportunity to show that you learn," he said.
"When you know and you meet some people, always you start to assess him from the day you meet them and for me we start from [here].
"Serge is a player with a lot of experience in Europe. Last season he was playing with Paris Saint-Germain in the Champions League.
"He will be good competition for Kyle [Walker-Peters] and [Kieran] Trippier in that position. It is a position we need to improve and I am happy.
"He is still young, only 24, but with a lot of experience. Now it is important he arrives here and adapts with the new squad.
"The Premier League is completely different to Ligue 1."