The Chilean returned to his homeland for friendlies with Peru and Bolivia and played the full 90 minutes in both, scoring a stoppage-time penalty to rescue a 2-2 draw against the latter.
Vidal has had problems with a knee injury in the past, and required surgery ahead of the World Cup in Brazil.
Perhaps with that and with the midfielder's gruelling international schedule in mind, Allegri has decided the 27-year-old will not face Sassuolo at the weekend.
"Vidal will not be in the squad," the coach said.
"He was late back yesterday, but it wasn't his fault. He came in and trained with the squad.
"Vidal has played two 90 minute games - and I don't think the Chilean coach played Vidal when he wasn't fit, he played two 90 minute games because he was in good condition.
"So, let's get rid of any controversy or potential controversy.
"However, having looked at the data Vidal isn't in as good a condition as the rest of the team.
"Given that he only came back yesterday, having just played two games and we have an important game in Athens on Wednesday [against Olympiacos in the UEFA Champions League], I'd prefer him to do three days of work here, so he will stay here in Turin."