The Portugal international was seen gesturing towards fans - mimicking Diego Simeone from the first leg after which the Atlético manager was fined €20,000 for an “obscene” celebration.
It came after Ronaldo converted a late penalty for his hat-trick and a 3-0 victory which sent the Serie A side through on aggregate.
“Disciplinary proceedings have been opened following the UEFA Champions League round of 16 match between Juventus Football Club and Club Atlético de Madrid, played on 12 March in Italy,” said a UEFA statement.
“Charges against Juventus Football Club: Improper conduct of player Cristiano Ronaldo.”
The case will be heard by the UEFA control, ethics and disciplinary body.