Alli stuck his middle finger up during the national side's World Cup qualifier against Slovakia on Monday but said after the game the gesture had been directed at teammate Kyle Walker as a joke.
But a FIFA spokesman said the incident was being investigated.
"We can confirm that disciplinary proceedings have been opened following this incident. Please understand we cannot comment further at this stage," the spokesman said.
Pictures and video footage of Alli's gesture were widely shared on social media but England manager Gareth Southgate played down the incident.
"The pair of them have a strange way of communicating! But that's what they've said when it's been raised."
Spurs boss Mauricio Pochettino, speaking on Thursday, had also played it down.
"It's true it's not a fantastic gesture but it's not a big issue. It was a joke in a moment with his teammate. I don't think it'll be a big issue with FIFA or with us."
Alli, 21, has had a number of run-ins with the football authorities and has faced calls to curb his fiery temperament.
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