Alli was hit with the punishment and fined 5,000 Swiss francs (£3,800) by world governing body FIFA following the incident in England’s win at Wembley last month.
Television footage showed the Tottenham midfielder making a middle-finger salute shortly after a collision with Martin Skrtel.
But Alli claimed the gesture was aimed at England team-mate Kyle Walker rather than the officials or any Slovakia player.
FIFA’s disciplinary committee accepted the 21-year-old was not taunting referee Clement Turpin, but still handed out the suspension.
Alli is set to miss next Thursday’s game against Slovenia at Wembley as England look to seal their place at next year’s World Cup,
He could return for the final group game in Lithuania on Sunday.
“Following the incident that occurred during the match between England and Slovakia on 4 September 2017. Dele Alli has been sanctioned with a suspension for one official match, and a fine of CHF 5,000 for making an offensive and unsporting gesture,” a FIFA spokesman said.
“Although the Disciplinary Committee was not convinced that the player directed the gesture at the referee, and regardless of whether it was allegedly directed at a team-mate, it did consider such gesture to be offensive and unsporting and therefore it amounted to a violation of art. 57 of the FIFA Disciplinary Code.”
Prior to the suspension being announced, England manager Gareth Southgate said he hoped Alli would learn from his mistake.
“I’ve had a good chat with Dele about a lot of different things but the biggest disappointment for him is to miss football,” Southgate told the FA website.
“So the upshot of all of this is that he recognises the responsibility and it’s important for him and us that he’s available for games which he wants to play.
“He’s a young player, a young man and young people are going to make mistakes – old people make plenty of mistakes.
“For certain, he knows something like what happened that night won’t happen again.”