It was the striker's first game back for the national team since the 2018 World Cup, but he was forced to sit out their 1-1 draw with Serbia the following Monday.
After the Serbia game, the 34-year-old insisted the issue was not serious and said he hoped to be fit in time for the first leg against Ajax on April 10, telling reporters: "I know I should be back in a week or two."
Runaway league leaders Juve face Empoli, Cagliari and AC Milan in Serie A action before heading to Amsterdam and Agnelli says the club's job is to protect the player, not put him at further risk by bringing him back too soon.
"When you have such injuries, you need to be careful," Agnelli said.
"Ronaldo is fine. We'll protect him from here until the end of the season because that's more important than thinking about a single match."
Ronaldo has made 36 appearances in all competitions for the Bianconeri this season, scoring 24 goals.
He was the hero in the last-16 of the Champions League as he grabbed a hat-trick to help Juve overcome a 2-0 first-leg deficit and knock Atletico Madrid out of the competition.
The five-time Ballon d'Or winner will be looking to win a fourth successive European Cup come May, having previously won three in a row at former club Real Madrid.
Juventus are on course for a double this season, with a huge 15 point lead to over Napoli to protect at the top of the Serie A table.