A Fifa spokesman said disciplinary proceedings had been opened against Juventus amid reports that the agreement struck between Pogba's agent, Mino Raiola, and the Serie A giants breached third-party ownership rules.
Fifa began investigating the Pogba transfer after the Times reported in May that Raiola would earn as much as £41m ($52m) from the Frenchman's £89m move to Old Trafford last summer.
The governing body had asked United and Juventus to submit all the relevant documents with regards to the transfer that made Pogba the most expensive player in football history.
A Fifa spokesman told ESPN: "We can confirm that disciplinary proceedings have been opened against Juventus FC. We cannot comment further as proceedings are ongoing.
"We can confirm that no disciplinary proceedings have been opened against Manchester United."
If found guilty, Juventus could face penalties ranging from a fine to a transfer ban.
Pogba, 24, spent three years in the youth team at United between 2009 and 2012, before leaving Old Trafford to join Juventus as a free agent.
The midfielder started 29 league games for the Red Devils last season, scoring five goals. He also scored against Ajax in the Europa League final to help United win the European trophy for the first time in their history.
Raiola insisted earlier this week that the Pogba transfer had fallen within Fifa guidelines and that he had not broken any rules.
"Fifa certainly didn't open any investigation into Paul's transfer to United," he was reported as saying by the Independent.
"Paul also acted correctly. When [Juventus general manager Giuseppe] Marotta asked us to stay in 2015, he did so in the right way.
"It's very true that the year after, Pogba left with the satisfaction of all concerned."