The 32-year-old was booked for dissent after complaining to the referee, and left the pitch in protest during stoppage time, leaving his team to play the last few minutes of the Serie A match at Cagliari with 10 men.
"@MuntariOfficial won! His ban has been overturned tonight," the union said in a tweet.
The decision to penalise the Ghanaian midfielder had drawn widespread criticism.
Other players condemned it and British anti-discrimination group Kick It Out called Italy's football authorities "gutless", while U.N. High Commissioner for Human Rights Zeid Ra'ad al-Hussein described Muntari as an inspiration.
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Italy and some other countries have struggled to stamp out racist chants at games. Lazio and Inter Milan were found guilty of racist behaviour by their fans during other games and warned they would face partial stadium closures if it continued.
Muntari said he had complained that parts of the crowd, including children, had hurled racist insults at him from the start of the match.
After the incident, FIFPro urged Italian authorities to "take firm action to ensure this never happens again".
(Reporting by Isla Binnie; editing by John Stonestreet)
