The Lausanne-based tribunal said on Tuesday it had registered the protest, although it could not yet give a date for the hearing and decision.
Cape Verde, who beat Tunisia 2-0 away to finish top of African Group B, forfeited the match after FIFA ruled that defender Fernando Varela had been ineligible to play.
Tunisia were awarded a 3-0 win which put them top of the group and into the playoff round in Cape Verde's place.
The Tunisians have already played the first leg of their playoff, drawing 0-0 at home to Cameroon last month.
Varela was banned for four matches after being sent off in an earlier Group B game against Equatorial Guinea, which Cape Verde lost 4-3.
That result itself was overturned, and the game awarded to Cape Verde 3-0, after FIFA ruled that Equatorial Guinea's Emilio Nsue, who scored a hat-trick, was not eligible to play.
Cape Verde argued that the red card and subsequent ban should not have counted as the match had been declared void.
(Writing by Brian Homewood; Editing by John O'Brien)
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