Ronaldo netted both goals for the Bianconeri in the club's 2-1 Coppa Italia semi-final first-leg win over Inter Milan on Tuesday but missed out on the chance to score his hat-trick after being substituted off in the 77th-minute of the encounter.
The five-time Ballon d'Or winner was visibly annoyed to see his number come up on the fourth official's board and was seen seemingly voicing his disapproval with Pirlo on the sidelines, but the Italian manager has since played down the 35-year-old's reaction.
"There is no contract clause that says he can't be subbed off. He knows he is a fundamental player for us but to get his breath back, he must always be at the top. He proved it with his performances after some criticism. He couldn't have done better than that.
"I said [to him] that he had to rest, we have an important match on Saturday. He has played many consecutive games, every now and then a little rest is good for him."
Ronaldo's brace took his overall tally for the season to 22 goals in just 23 appearances across all competitions, and he is now just 13 strikes away from potentially becoming the fastest player to reach a century of goals for the Italian giants.