The matter will be investigated and submitted to FIFA's disciplinary committee.
The Tottenham Hotspur player was caught on camera raising a middle finger in the direction of French referee Clement Turpin after the official did not award a foul for a heavy challenge by Slovakia's Martin Skrtel late in the match last Monday.
England won the Group F qualifier 2-1.
England manager Gareth Southgate said the 21-year-old had told him the gesture was made in jest towards his former Tottenham team mate Kyle Walker, who joined Manchester City over the summer.
"Kyle and Dele were mucking about, and Dele's made a gesture towards Kyle. I don't know what the angle of the pitch is. The pair of them have a strange way of communicating, but that's what they've said," he told reporters.
Alli, who was praised by Southgate for his match performance, later explained his actions on Twitter.
"Just to clarify, the gesture tonight was a joke between me and my good friend Kyle Walker! Apologies for any offence caused! Great win 2nite (sic)," he wrote.
(Reporting by Alan Baldwin, editing by Amlan Chakraborty)
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