Cape Verde had topped Group B of African qualifying after their 2-0 win over Nabil Maaloul's men in Rades on Saturday.
However, FIFA found the Cape Verdean Football Association guilty of fielding Fernando Varela, despite the player not having served a full four-match suspension for a red card.
As a result, Tunisia have been awarded a 3-0 win by default - enough to move them top ahead of Cape Verde and see them advance to the next stage.
A FIFA statement read: "The match has been declared to be forfeited and awarded 3-0 in favour of Tunisia.
"The Cape Verde Islands will not progress to round three of the FIFA World Cup African zone qualifiers having dropped to second place in Group B with nine points while Tunisia finish first with 14 points and will now advance."
The draw for round three is due to take place on Monday.
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