The France midfielder returned to United in a deal worth more than $111 million, 105.2 million euros) in August 2016 from the Italian giants.
In May FIFA began an inquiry into the move, requesting information about the headline transfer from United.
But in a statement FIFA confirmed that while United were in the clear of any wrongdoing, they were taking action against Juventus.
“We can confirm that disciplinary proceedings have been opened against Juventus FC.
“We can also confirm that no disciplinary proceedings have been opened against Manchester United,” the statement said.
It added: “As proceedings are ongoing please understand we cannot comment further at this stage.”
Pogba’s move came under particular scrutiny amid reports the player’s agent Mino Raiola would earn some 49 million euros from the deal.
Raiola is suspected of a conflict of interest, as he was at the time agent for Pogba, Juventus and Manchester United.
In May, French website Mediapart, quoting the Football Leaks documents, claimed: “Pogba in reality cost 127 million euros to Manchester United with 49 millions going into Raiola’s pockets and only 78 millions into Juve’s bank account.”
According to the investigative site, Raiola “didn’t appear to let Manchester United know that he was also working for Juventus,” an arrangement that is outlawed under English rules.
Pogba, 24, started his career with United but made just three appearances in the Premier League before heading to Italy, after an apparent falling out with then manager Alex Ferguson.
He flourished in Serie A, winning four league titles with Juventus between 2012 and 2016.
Pogba appeared in the 2015 Champions League final, which Juventus lost 3-1 to Barcelona.
At the same time, the powerful midfielder made himself a mainstay of the French national team.
He made his debut in March 2013, just a week after his 20th birthday, in a World Cup qualifier against Georgia.
He also featured as part of the 2014 French World Cup squad and was named the tournament’s best young player.
Pogba’s performances at the 2016 European Championship helped attract the attention of his former club Manchester United, under new manager Jose Mourinho.
Last season he helped propel United to a first ever Europa League title, scoring in his team’s 2-0 victory over Ajax in Stockholm on May 25.