Alli stuck his middle finger up during the national side’s match against Slovakia on Monday but said after the game the hand signal had been directed at teammate Kyle Walker as a joke.
Following initial investigations, which are expected to have included reviewing the referee’s official match report, the world governing body said Alli would have a case to answer.
“We can confirm that disciplinary proceedings have been opened following this incident. Please understand we cannot comment further at this stage,” a FIFA spokesman said.
The Football Association has been given until September 13 to respond, and it is understood the national body has more television coverage of the incident, yet to be broadcast, which could be presented to back up Alli’s stance.
Pictures and video footage of the gesture were widely shared on social media but England manager Gareth Southgate played down the incident.
“Kyle and Dele were mucking about and Dele’s made a gesture towards Kyle,” Southgate told reporters at Wembley after England’s 2-1 win.
“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.
He missed the Premier League title run-in in 2015-16 after punching West Bromwich Albion’s Claudio Yacob and was sent off for a dangerous foul on Gent’s Brecht Dejaegere during a Europa League game in February.
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