The incident happened during the second half of the Three Lions' 2-1 victory on Monday, which left the Gareth Southgate's men on the verge of World Cup qualification.
Alli appeared to gesture in the direction of referee Clement Turpin after nothing was awarded following a challenge on the Tottenham man from from Martin Skrtel.
But Alli claimed on social media afterwards the middle-finger salute was in fact "a joke" between himself and former Spurs team-mate Kyle Walker.
And England manager Southgate backed up the claim in his post-match press conference. He said: "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 when it's been raised."
A wider clip with both players in shot shows Walker is standing on the halfway line in a similar direction to the referee, adding weight to Alli's claim.
But the 21-year-old could be slapped with a fine and a ban by Fifa if it is deemed the gesture was indeed directed at the official.
And if Turpin fails to address the matter in his post-match report, the threat of suspension still looms for the Tottenham man if the incident is considered "serious misconduct".
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England's final two qualification matches are their last competitive games before next summer's World Cup and if Alli is served with a ban of more than two matches, he will miss the beginning of next summer's showpiece in Russia.
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